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PDBsum entry 1dog

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Hydrolase PDB id
1dog
Jmol
Contents
Protein chain
470 a.a.
Ligands
NAG-NAG-BMA-MAN-
MAN
NAG-NAG-BMA-MAN-
MAN-MAN-MAN-MAN
MAN ×10
NOJ ×2
Waters ×605
HEADER    HYDROLASE                               12-JAN-93   1DOG
TITLE     REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH
TITLE    2 GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS
TITLE    3 RESOLUTION
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: GLUCOAMYLASE-471;
COMPND   3 CHAIN: A;
COMPND   4 EC: 3.2.1.3;
COMPND   5 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: ASPERGILLUS AWAMORI;
SOURCE   3 ORGANISM_TAXID: 105351
KEYWDS    HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    E.HARRIS,A.ALESHIN,L.FIRSOV,R.B.HONZATKO
REVDAT   5   13-JUL-11 1DOG    1       VERSN
REVDAT   4   24-FEB-09 1DOG    1       VERSN
REVDAT   3   01-APR-03 1DOG    1       JRNL
REVDAT   2   30-APR-94 1DOG    1       REMARK
REVDAT   1   31-JAN-94 1DOG    0
JRNL        AUTH   E.M.HARRIS,A.E.ALESHIN,L.M.FIRSOV,R.B.HONZATKO
JRNL        TITL   REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH
JRNL        TITL 2 GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100 TO 2.4-A
JRNL        TITL 3 RESOLUTION.
JRNL        REF    BIOCHEMISTRY                  V.  32  1618 1993
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   8431441
JRNL        DOI    10.1021/BI00057A028
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   A.ALESHIN,A.GOLUBEV,L.M.FIRSOV,R.B.HONZATKO
REMARK   1  TITL   CRYSTAL STRUCTURE OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI
REMARK   1  TITL 2 VAR. X100 TO 2.2-A RESOLUTION
REMARK   1  REF    J.BIOL.CHEM.                  V. 267 19291 1992
REMARK   1  REFN                   ISSN 0021-9258
REMARK   2
REMARK   2 RESOLUTION.    2.30 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PROLSQ
REMARK   3   AUTHORS     : KONNERT,HENDRICKSON
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 10.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 1.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : NULL
REMARK   3   NUMBER OF REFLECTIONS             : NULL
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.119
REMARK   3   R VALUE            (WORKING SET) : NULL
REMARK   3   FREE R VALUE                     : NULL
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3562
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 287
REMARK   3   SOLVENT ATOMS            : 605
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   DISTANCE RESTRAINTS.                    RMS    SIGMA
REMARK   3    BOND LENGTH                     (A) : 0.012 ; 0.020
REMARK   3    ANGLE DISTANCE                  (A) : 0.030 ; 0.030
REMARK   3    INTRAPLANAR 1-4 DISTANCE        (A) : 0.040 ; 0.050
REMARK   3    H-BOND OR METAL COORDINATION    (A) : NULL  ; NULL
REMARK   3
REMARK   3   PLANE RESTRAINT                  (A) : 0.012 ; 0.020
REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) : 0.137 ; 0.150
REMARK   3
REMARK   3   NON-BONDED CONTACT RESTRAINTS.
REMARK   3    SINGLE TORSION                  (A) : 0.225 ; 0.250
REMARK   3    MULTIPLE TORSION                (A) : 0.159 ; 0.250
REMARK   3    H-BOND (X...Y)                  (A) : NULL  ; NULL
REMARK   3    H-BOND (X-H...Y)                (A) : 0.201 ; 0.250
REMARK   3
REMARK   3   CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK   3    SPECIFIED                 (DEGREES) : NULL  ; NULL
REMARK   3    PLANAR                    (DEGREES) : 2.200 ; 3.000
REMARK   3    STAGGERED                 (DEGREES) : 14.200; 10.000
REMARK   3    TRANSVERSE                (DEGREES) : NULL  ; NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND               (A**2) : 0.605 ; 1.000
REMARK   3   MAIN-CHAIN ANGLE              (A**2) : 1.037 ; 1.500
REMARK   3   SIDE-CHAIN BOND               (A**2) : 1.865 ; 2.000
REMARK   3   SIDE-CHAIN ANGLE              (A**2) : 2.817 ; 3.000
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1DOG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : NULL
REMARK 200  PH                             : NULL
REMARK 200  NUMBER OF CRYSTALS USED        : NULL
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : NULL
REMARK 200  RADIATION SOURCE               : NULL
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : NULL
REMARK 200  WAVELENGTH OR RANGE        (A) : NULL
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : NULL
REMARK 200  DETECTOR MANUFACTURER          : NULL
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200  DATA SCALING SOFTWARE          : NULL
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : NULL
REMARK 200  RESOLUTION RANGE HIGH      (A) : NULL
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 57.44
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X+1/2,-Y,Z+1/2
REMARK 290       3555   -X,Y+1/2,-Z+1/2
REMARK 290       4555   X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       58.30000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       24.15000
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       51.80000
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       24.15000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       58.30000
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       51.80000
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 400
REMARK 400 COMPOUND
REMARK 400 ACTIVE SITE:  (SEE TABLE II OF MANUSCRIPT AND THE
REMARK 400 DISCUSSION CONCERNING THE CATALYTIC MECHANISM) RESIDUES
REMARK 400 THAT BIND TO 1-DEOXYNOJIRIMYCIN AT ITS PRINCIPAL SITE ARE
REMARK 400 ASP 55 OD1, ASP 55 OD2, ARG 305 NH1, CARBONYL 177, ARG 54
REMARK 400 NE, AND ARG 54 NH2.  GLU 179 IS THE CATALYTIC ACID AND
REMARK 400 RESIDUE GLU 400 IS THE CATALYTIC BASE.  WATER 1201 IS THE
REMARK 400 NUCLEOPHILE.
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    ARG A  68   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 DEGREES
REMARK 500    ARG A  68   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.4 DEGREES
REMARK 500    ARG A 122   NE  -  CZ  -  NH2 ANGL. DEV. =   5.0 DEGREES
REMARK 500    ARG A 160   CD  -  NE  -  CZ  ANGL. DEV. =   8.9 DEGREES
REMARK 500    ARG A 160   NE  -  CZ  -  NH1 ANGL. DEV. =   4.2 DEGREES
REMARK 500    ARG A 160   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.5 DEGREES
REMARK 500    ARG A 194   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.1 DEGREES
REMARK 500    ARG A 273   NE  -  CZ  -  NH1 ANGL. DEV. =   8.9 DEGREES
REMARK 500    ARG A 273   NE  -  CZ  -  NH2 ANGL. DEV. =  -8.2 DEGREES
REMARK 500    ARG A 286   NE  -  CZ  -  NH1 ANGL. DEV. =   3.9 DEGREES
REMARK 500    TYR A 289   CB  -  CG  -  CD1 ANGL. DEV. =   3.8 DEGREES
REMARK 500    LEU A 341   CA  -  CB  -  CG  ANGL. DEV. =  19.7 DEGREES
REMARK 500    ASP A 406   CB  -  CG  -  OD1 ANGL. DEV. =   6.0 DEGREES
REMARK 500    ARG A 413   NE  -  CZ  -  NH1 ANGL. DEV. =   3.6 DEGREES
REMARK 500    ARG A 428   NE  -  CZ  -  NH1 ANGL. DEV. =   4.9 DEGREES
REMARK 500    ARG A 428   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.2 DEGREES
REMARK 500    ARG A 429   NE  -  CZ  -  NH1 ANGL. DEV. =   4.4 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    ASN A  45       72.86     40.29
REMARK 500    GLU A 113       15.31     84.49
REMARK 500    TYR A 147       52.33   -110.10
REMARK 500    ILE A 154      -64.93   -105.17
REMARK 500    ASN A 171       23.71    -77.55
REMARK 500    SER A 208     -158.72   -119.37
REMARK 500    ASP A 238       33.45     89.63
REMARK 500    TYR A 312       19.68     57.06
REMARK 500    ASN A 313       -6.22     99.17
REMARK 500    SER A 411     -152.95     66.80
REMARK 500    ASP A 414       57.43     39.22
REMARK 500    ALA A 442       47.38   -145.64
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        RMS     TYPE
REMARK 500    ARG A 428         0.12    SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        ANGLE
REMARK 500    THR A 246        -12.37
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A1039        DISTANCE =  6.20 ANGSTROMS
REMARK 525    HOH A1042        DISTANCE =  6.28 ANGSTROMS
REMARK 525    HOH A1067        DISTANCE =  5.69 ANGSTROMS
REMARK 525    HOH A1076        DISTANCE =  5.44 ANGSTROMS
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 THERE ARE SOME CLOSE CONTACTS BETWEEN WATERS AND THE
REMARK 600 DEOXYNOJIRIMYCIN MOLECULE WHICH ARE THE RESULT OF THE
REMARK 600 CO-REFINEMENT OF AN INHIBITOR MOLECULE AT LESS THAN FULL
REMARK 600 OCCUPANCY ALONG WITH SOLVENT MOLECULES WHICH ARE PRESENT
REMARK 600 IN THE ABSENCE OF THE INHIBITOR.  THE PAPER CITED ON JRNL
REMARK 600 RECORDS ABOVE DISCUSSES THIS BRIEFLY IN THE METHODS
REMARK 600 SECTION.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 472A
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 473B
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMA A 474C
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 475D
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 476G
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 477A
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 478B
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMA A 479C
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 480D
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 481G
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 482E
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 483F
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 484H
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 485
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 486
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 487
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 488
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 489
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 490
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 491
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 492
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 493
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 494
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NOJ A 495
REMARK 800
REMARK 800 SITE_IDENTIFIER: CC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NOJ A 496
DBREF  1DOG A    1   471  UNP    P23176   AMYG_ASPAK      25    494
SEQADV 1DOG LEU A   58  UNP  P23176    ILE    82 CONFLICT
SEQADV 1DOG ILE A   60  UNP  P23176    LEU    84 CONFLICT
SEQADV 1DOG THR A  117  UNP  P23176    ALA   140 CONFLICT
SEQRES   1 A  470  ALA THR LEU ASP SER TRP LEU SER ASN GLU ALA THR VAL
SEQRES   2 A  470  ALA ARG THR ALA ILE LEU ASN ASN ILE GLY ALA ASP GLY
SEQRES   3 A  470  ALA TRP VAL SER GLY ALA ASP SER GLY ILE VAL VAL ALA
SEQRES   4 A  470  SER PRO SER THR ASP ASN PRO ASP TYR PHE TYR THR TRP
SEQRES   5 A  470  THR ARG ASP SER GLY LEU VAL ILE LYS THR LEU VAL ASP
SEQRES   6 A  470  LEU PHE ARG ASN GLY ASP THR ASP LEU LEU SER THR ILE
SEQRES   7 A  470  GLU HIS TYR ILE SER SER GLN ALA ILE ILE GLN GLY VAL
SEQRES   8 A  470  SER ASN PRO SER GLY ASP LEU SER SER GLY GLY LEU GLY
SEQRES   9 A  470  GLU PRO LYS PHE ASN VAL ASP GLU THR ALA TYR THR GLY
SEQRES  10 A  470  SER TRP GLY ARG PRO GLN ARG ASP GLY PRO ALA LEU ARG
SEQRES  11 A  470  ALA THR ALA MET ILE GLY PHE GLY GLN TRP LEU LEU ASP
SEQRES  12 A  470  ASN GLY TYR THR SER ALA ALA THR GLU ILE VAL TRP PRO
SEQRES  13 A  470  LEU VAL ARG ASN ASP LEU SER TYR VAL ALA GLN TYR TRP
SEQRES  14 A  470  ASN GLN THR GLY TYR ASP LEU TRP GLU GLU VAL ASN GLY
SEQRES  15 A  470  SER SER PHE PHE THR ILE ALA VAL GLN HIS ARG ALA LEU
SEQRES  16 A  470  VAL GLU GLY SER ALA PHE ALA THR ALA VAL GLY SER SER
SEQRES  17 A  470  CYS SER TRP CYS ASP SER GLN ALA PRO GLN ILE LEU CYS
SEQRES  18 A  470  TYR LEU GLN SER PHE TRP THR GLY SER TYR ILE LEU ALA
SEQRES  19 A  470  ASN PHE ASP SER SER ARG SER GLY LYS ASP THR ASN THR
SEQRES  20 A  470  LEU LEU GLY SER ILE HIS THR PHE ASP PRO GLU ALA GLY
SEQRES  21 A  470  CYS ASP ASP SER THR PHE GLN PRO CYS SER PRO ARG ALA
SEQRES  22 A  470  LEU ALA ASN HIS LYS GLU VAL VAL ASP SER PHE ARG SER
SEQRES  23 A  470  ILE TYR THR LEU ASN ASP GLY LEU SER ASP SER GLU ALA
SEQRES  24 A  470  VAL ALA VAL GLY ARG TYR PRO GLU ASP SER TYR TYR ASN
SEQRES  25 A  470  GLY ASN PRO TRP PHE LEU CYS THR LEU ALA ALA ALA GLU
SEQRES  26 A  470  GLN LEU TYR ASP ALA LEU TYR GLN TRP ASP LYS GLN GLY
SEQRES  27 A  470  SER LEU GLU ILE THR ASP VAL SER LEU ASP PHE PHE LYS
SEQRES  28 A  470  ALA LEU TYR SER GLY ALA ALA THR GLY THR TYR SER SER
SEQRES  29 A  470  SER SER SER THR TYR SER SER ILE VAL SER ALA VAL LYS
SEQRES  30 A  470  THR PHE ALA ASP GLY PHE VAL SER ILE VAL GLU THR HIS
SEQRES  31 A  470  ALA ALA SER ASN GLY SER LEU SER GLU GLN PHE ASP LYS
SEQRES  32 A  470  SER ASP GLY ASP GLU LEU SER ALA ARG ASP LEU THR TRP
SEQRES  33 A  470  SER TYR ALA ALA LEU LEU THR ALA ASN ASN ARG ARG ASN
SEQRES  34 A  470  SER VAL VAL PRO PRO SER TRP GLY GLU THR SER ALA SER
SEQRES  35 A  470  SER VAL PRO GLY THR CYS ALA ALA THR SER ALA SER GLY
SEQRES  36 A  470  THR TYR SER SER VAL THR VAL THR SER TRP PRO SER ILE
SEQRES  37 A  470  VAL ALA
MODRES 1DOG ASN A  171  ASN  GLYCOSYLATION SITE
MODRES 1DOG ASN A  395  ASN  GLYCOSYLATION SITE
MODRES 1DOG SER A  443  SER  GLYCOSYLATION SITE
MODRES 1DOG SER A  444  SER  GLYCOSYLATION SITE
MODRES 1DOG THR A  452  THR  GLYCOSYLATION SITE
MODRES 1DOG SER A  453  SER  GLYCOSYLATION SITE
MODRES 1DOG SER A  455  SER  GLYCOSYLATION SITE
MODRES 1DOG THR A  457  THR  GLYCOSYLATION SITE
MODRES 1DOG SER A  459  SER  GLYCOSYLATION SITE
MODRES 1DOG SER A  460  SER  GLYCOSYLATION SITE
MODRES 1DOG THR A  462  THR  GLYCOSYLATION SITE
MODRES 1DOG THR A  464  THR  GLYCOSYLATION SITE
HET    NAG  A 472A     14
HET    NAG  A 473B     14
HET    BMA  A 474C     11
HET    MAN  A 475D     11
HET    MAN  A 476G     11
HET    NAG  A 477A     14
HET    NAG  A 478B     14
HET    BMA  A 479C     11
HET    MAN  A 480D     11
HET    MAN  A 481G     11
HET    MAN  A 482E     11
HET    MAN  A 483F     11
HET    MAN  A 484H     11
HET    MAN  A 485      11
HET    MAN  A 486      11
HET    MAN  A 487      11
HET    MAN  A 488      11
HET    MAN  A 489      11
HET    MAN  A 490      11
HET    MAN  A 491      11
HET    MAN  A 492      11
HET    MAN  A 493      11
HET    MAN  A 494      11
HET    NOJ  A 495      11
HET    NOJ  A 496      11
HETNAM     NAG N-ACETYL-D-GLUCOSAMINE
HETNAM     BMA BETA-D-MANNOSE
HETNAM     MAN ALPHA-D-MANNOSE
HETNAM     NOJ 1-DEOXYNOJIRIMYCIN
HETSYN     NOJ MORANOLINE
FORMUL   2  NAG    4(C8 H15 N O6)
FORMUL   2  BMA    2(C6 H12 O6)
FORMUL   2  MAN    17(C6 H12 O6)
FORMUL  14  NOJ    2(C6 H13 N O4)
FORMUL  16  HOH   *605(H2 O)
HELIX    1  H1 ALA A    1  ASN A   20  1                                  20
HELIX    2  H2 THR A   53  ARG A   68  1                                  16
HELIX    3  H3 THR A   72  GLN A   89  1                                  18
HELIX    4  H4 ASP A  126  ASP A  144  1                                  19
HELIX    5  H5 THR A  148  GLN A  168  1                                  21
HELIX    6  H6 PHE A  186  ALA A  205  1                                  20
HELIX    7  H7 SER A  211  PHE A  227  1                                  17
HELIX    8  H8 ASP A  245  HIS A  254  1                                  10
HELIX    9  H9 PRO A  272  PHE A  285  1                                  14
HELIX   10 H10 PHE A  318  GLN A  338  1                                  21
HELIX   11 H11 ASP A  345  LEU A  354  1NOT PART OF THE BARREL            10
HELIX   12 H12 SER A  368  HIS A  391  1                                  24
HELIX   13 H13 THR A  416  ARG A  429  1                                  14
SHEET    1  S1 2 ASN A  21  GLY A  23  0
SHEET    2  S1 2 GLY A  35  VAL A  38 -1  O  ILE A  36   N  GLY A  23
SHEET    1  S2 3 PHE A  49  THR A  53  0
SHEET    2  S2 3 PRO A 107  ASN A 110 -1  O  PHE A 109   N  THR A  51
SHEET    3  S2 3 GLU A 113  TYR A 116 -1  O  THR A 114   N  ASN A 110
SHEET    1  S3 2 VAL A  91  ASN A  93  0
SHEET    2  S3 2 GLY A  96  ASP A  97 -1  O  GLY A  96   N  ASN A  93
SHEET    1  S4 2 THR A 173  ASP A 176  0
SHEET    2  S4 2 VAL A 181  GLY A 183 -1  N  GLY A 183   O  GLY A 174
SHEET    1  S5 2 SER A 184  SER A 185  0
SHEET    2  S5 2 ALA A 235  PHE A 237 -1  N  PHE A 237   O  SER A 184
SHEET    1  S6 2 CYS A 262  ASP A 264  0
SHEET    2  S6 2 PHE A 267  GLN A 268 -1  N  PHE A 267   O  ASP A 264
SHEET    1  S7 2 GLY A 339  THR A 344  0
SHEET    2  S7 2 THR A 360  SER A 365 -1  N  TYR A 363   O  LEU A 341
SHEET    1  S8 2 ALA A 392  ALA A 393  0
SHEET    2  S8 2 GLY A 396  SER A 397 -1  N  GLY A 396   O  ALA A 393
SHEET    1  S9 2 LEU A 398  ASP A 403  0
SHEET    2  S9 2 GLY A 407  LEU A 415 -1  O  ALA A 412   N  GLU A 400
SSBOND   1 CYS A  210    CYS A  213                          1555   1555  2.00
SSBOND   2 CYS A  222    CYS A  449                          1555   1555  1.98
SSBOND   3 CYS A  262    CYS A  270                          1555   1555  2.04
LINK         ND2 ASN A 171                 C1  NAG A 472A    1555   1555  1.39
LINK         ND2 ASN A 395                 C1  NAG A 477A    1555   1555  1.37
LINK         OG  SER A 443                 C1  MAN A 485     1555   1555  1.36
LINK         OG  SER A 444                 C1  MAN A 486     1555   1555  1.39
LINK         OG1 THR A 452                 C1  MAN A 487     1555   1555  1.39
LINK         OG  SER A 453                 C1  MAN A 488     1555   1555  1.36
LINK         OG  SER A 455                 C1  MAN A 489     1555   1555  1.39
LINK         OG1 THR A 457                 C1  MAN A 490     1555   1555  1.41
LINK         OG  SER A 459                 C1  MAN A 491     1555   1555  1.39
LINK         OG  SER A 460                 C1  MAN A 492     1555   1555  1.40
LINK         OG1 THR A 462                 C1  MAN A 493     1555   1555  1.39
LINK         OG1 THR A 464                 C1  MAN A 494     1555   1555  1.40
LINK         O4  NAG A 472A                C1  NAG A 473B    1555   1555  1.38
LINK         O4  NAG A 473B                C1  BMA A 474C    1555   1555  1.39
LINK         O3  BMA A 474C                C1  MAN A 475D    1555   1555  1.37
LINK         O2  MAN A 475D                C1  MAN A 476G    1555   1555  1.38
LINK         O4  NAG A 477A                C1  NAG A 478B    1555   1555  1.39
LINK         O4  NAG A 478B                C1  BMA A 479C    1555   1555  1.39
LINK         O3  BMA A 479C                C1  MAN A 480D    1555   1555  1.39
LINK         O6  BMA A 479C                C1  MAN A 482E    1555   1555  1.39
LINK         O2  MAN A 480D                C1  MAN A 481G    1555   1555  1.39
LINK         O2  MAN A 481G                C1  MAN A 484H    1555   1555  1.38
LINK         O3  MAN A 482E                C1  MAN A 483F    1555   1555  1.40
CISPEP   1 GLY A   23    ALA A   24          0         0.21
CISPEP   2 ASN A   45    PRO A   46          0        -1.95
CISPEP   3 ARG A  122    PRO A  123          0        -1.10
SITE     1 AC1 12 ASN A 171  THR A 173  SER A 184  TYR A 223
SITE     2 AC1 12 CYS A 449  ALA A 451  NAG A 473B HOH A 515
SITE     3 AC1 12 HOH A 527  HOH A 655  HOH A 660  HOH A 718
SITE     1 AC2  5 PHE A 237  CYS A 449  NAG A 472A BMA A 474C
SITE     2 AC2  5 HOH A 655
SITE     1 AC3  2 NAG A 473B MAN A 475D
SITE     1 AC4  4 SER A 226  PHE A 237  BMA A 474C MAN A 476G
SITE     1 AC5  6 ASN A 236  PHE A 237  ASP A 238  SER A 239
SITE     2 AC5  6 MAN A 475D HOH A 739
SITE     1 AC6  6 TRP A  28  ASN A 395  SER A 397  ASP A 414
SITE     2 AC6  6 NAG A 478B HOH A 700
SITE     1 AC7  8 ARG A 413  NAG A 477A BMA A 479C MAN A 482E
SITE     2 AC7  8 MAN A 483F HOH A 513  HOH A 700  HOH A 791
SITE     1 AC8  7 ARG A 413  NAG A 478B MAN A 480D MAN A 482E
SITE     2 AC8  7 HOH A 688  HOH A 706  HOH A 854
SITE     1 AC9  4 BMA A 479C MAN A 481G HOH A 813  HOH A 893
SITE     1 BC1  9 SER A  30  PRO A  41  THR A  43  PHE A  49
SITE     2 BC1  9 MAN A 480D MAN A 484H HOH A 645  HOH A 744
SITE     3 BC1  9 HOH A 893
SITE     1 BC2  7 NAG A 478B BMA A 479C MAN A 483F HOH A 748
SITE     2 BC2  7 HOH A 785  HOH A 865  HOH A 935
SITE     1 BC3  9 SER A  42  ASN A  45  SER A 411  ARG A 413
SITE     2 BC3  9 NAG A 478B MAN A 482E HOH A 694  HOH A1035
SITE     3 BC3  9 HOH A1043
SITE     1 BC4  3 THR A  43  ASP A  44  MAN A 481G
SITE     1 BC5 12 ASP A 263  GLU A 439  THR A 440  SER A 441
SITE     2 BC5 12 ALA A 442  SER A 443  SER A 444  HOH A 623
SITE     3 BC5 12 HOH A 787  HOH A 949  HOH A 978  HOH A1097
SITE     1 BC6  5 SER A 444  PRO A 446  HOH A 585  HOH A 787
SITE     2 BC6  5 HOH A1013
SITE     1 BC7  7 THR A 452  SER A 453  HOH A 630  HOH A 678
SITE     2 BC7  7 HOH A 722  HOH A 866  HOH A1046
SITE     1 BC8  7 SER A 119  GLU A 153  GLN A 168  SER A 453
SITE     2 BC8  7 HOH A 783  HOH A 962  HOH A 995
SITE     1 BC9 11 TRP A 120  GLN A 168  TYR A 175  SER A 455
SITE     2 BC9 11 TYR A 458  HOH A 533  HOH A 552  HOH A 589
SITE     3 BC9 11 HOH A 930  HOH A 947  HOH A 997
SITE     1 CC1 12 ARG A 122  PRO A 123  ARG A 125  ARG A 160
SITE     2 CC1 12 THR A 173  GLY A 174  ASN A 182  THR A 457
SITE     3 CC1 12 MAN A 491  HOH A 544  HOH A 859  HOH A 888
SITE     1 CC2 12 PRO A 157  ARG A 160  GLN A 172  THR A 173
SITE     2 CC2 12 SER A 459  SER A 460  MAN A 490  HOH A 557
SITE     3 CC2 12 HOH A 608  HOH A 672  HOH A 693  HOH A 912
SITE     1 CC3  7 ALA A  86  ILE A  87  GLY A  90  SER A 460
SITE     2 CC3  7 VAL A 461  HOH A 646  HOH A 698
SITE     1 CC4  6 SER A 460  VAL A 461  THR A 462  MAN A 494
SITE     2 CC4  6 HOH A 776  HOH A 838
SITE     1 CC5  5 GLU A 153  THR A 462  THR A 464  MAN A 493
SITE     2 CC5  5 HOH A 778
SITE     1 CC6 13 ALA A  39  TYR A  48  TRP A  52  ARG A  54
SITE     2 CC6 13 ASP A  55  LEU A 177  TRP A 178  ARG A 305
SITE     3 CC6 13 TRP A 417  NOJ A 496  HOH A 501  HOH A 634
SITE     4 CC6 13 HOH A1202
SITE     1 CC7 12 LEU A 143  TRP A 178  GLU A 179  GLU A 180
SITE     2 CC7 12 ARG A 305  TYR A 311  NOJ A 495  HOH A 634
SITE     3 CC7 12 HOH A1064  HOH A1200  HOH A1201  HOH A1202
CRYST1  116.600  103.600   48.300  90.00  90.00  90.00 P 21 21 21    4
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.008576  0.000000  0.000000        0.00000
SCALE2      0.000000  0.009653  0.000000        0.00000
SCALE3      0.000000  0.000000  0.020704        0.00000
      
PROCHECK
Go to PROCHECK summary
 References