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PDBsum entry 1rpk

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Hydrolase PDB id
1rpk
Jmol
Contents
Protein chain
404 a.a.
Ligands
DAF-GLC ×2
DAF-GLC-GLC
Metals
_CA ×3
Waters ×549
HEADER    HYDROLASE                               03-DEC-03   1RPK
TITLE     CRYSTAL STRUCTURE OF BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1)
TITLE    2 IN COMPLEX WITH ACARBOSE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: ALPHA-AMYLASE TYPE 1 ISOZYME;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE, AMY1, LOW PI
COMPND   5 ALPHA-AMYLASE;
COMPND   6 EC: 3.2.1.1;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE;
SOURCE   3 ORGANISM_TAXID: 4513;
SOURCE   4 GENE: AMY1.1;
SOURCE   5 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 4922;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: GS115;
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PHIL-D2
KEYWDS    ALPHA-AMYLASE, BARLEY, ISOZYME 1, BETA-ALPHA-BARREL, X-RAY
KEYWDS   2 DIFFRACTION, SUGAR TONGS BINDING SITE, ACARBOSE, HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    X.ROBERT,R.HASER,N.AGHAJARI
REVDAT   4   24-FEB-09 1RPK    1       VERSN
REVDAT   3   04-OCT-05 1RPK    1       JRNL
REVDAT   2   09-AUG-05 1RPK    1       JRNL
REVDAT   1   07-JUN-05 1RPK    0
JRNL        AUTH   X.ROBERT,R.HASER,H.MORI,B.SVENSSON,N.AGHAJARI
JRNL        TITL   OLIGOSACCHARIDE BINDING TO BARLEY {ALPHA}-AMYLASE 1
JRNL        REF    J.BIOL.CHEM.                  V. 280 32968 2005
JRNL        REFN                   ISSN 0021-9258
JRNL        PMID   16030022
JRNL        DOI    10.1074/JBC.M505515200
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS 1.0
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : ENGH & HUBER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 17.36
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 1795456.560
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 94.2
REMARK   3   NUMBER OF REFLECTIONS             : 27308
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.180
REMARK   3   FREE R VALUE                     : 0.231
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 8.800
REMARK   3   FREE R VALUE TEST SET COUNT      : 2399
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.005
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 6
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.00
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.13
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 95.50
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 4300
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2350
REMARK   3   BIN FREE R VALUE                    : 0.3020
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 5.30
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 241
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.019
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3136
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 113
REMARK   3   SOLVENT ATOMS            : 549
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 5.50
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 13.80
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -1.09000
REMARK   3    B22 (A**2) : -2.25000
REMARK   3    B33 (A**2) : 3.34000
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.20
REMARK   3   ESD FROM SIGMAA              (A) : 0.20
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.27
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.25
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.010
REMARK   3   BOND ANGLES            (DEGREES) : 1.50
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 23.40
REMARK   3   IMPROPER ANGLES        (DEGREES) : 0.90
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : 1.360 ; 1.500
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : 1.840 ; 2.000
REMARK   3   SIDE-CHAIN BOND              (A**2) : 2.130 ; 2.000
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : 2.780 ; 2.500
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : FLAT MODEL
REMARK   3   KSOL        : 0.36
REMARK   3   BSOL        : 57.44
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : PROTEIN_REP.PARAM
REMARK   3  PARAMETER FILE  2  : WATER_REP.PARAM
REMARK   3  PARAMETER FILE  3  : ION.PARAM
REMARK   3  PARAMETER FILE  4  : PARAMACA.CHO
REMARK   3  PARAMETER FILE  5  : NULL
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.TOP
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP
REMARK   3  TOPOLOGY FILE  3   : ION.TOP
REMARK   3  TOPOLOGY FILE  4   : TOPH3_MOD.CHO
REMARK   3  TOPOLOGY FILE  5   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1RPK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-03.
REMARK 100 THE RCSB ID CODE IS RCSB020930.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 10-NOV-99
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 6.7
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : ROTATING ANODE
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : ENRAF-NONIUS FR591
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : OSMIC MIRRORS
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 27344
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.000
REMARK 200  RESOLUTION RANGE LOW       (A) : 17.360
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 100.0
REMARK 200  DATA REDUNDANCY                : 3.500
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.18300
REMARK 200   FOR THE DATA SET  : 4.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.05
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.10
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.66600
REMARK 200   FOR SHELL         : 1.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER DIFFERENCE
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: PDB ENTRY 1HT6
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 47.46
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, ISOPROPANOL, PH 6.7,
REMARK 280  VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z
REMARK 290       3555   -X+1/2,Y+1/2,-Z
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        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000       46.69500
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       36.46000
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       46.69500
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       36.46000
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     ASN A   405
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470   M RES CSSEQI  ATOMS
REMARK 470     LYS A 404    CG   CD   CE   NZ
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    CYS A 106       11.96   -141.82
REMARK 500    ASP A 114     -158.08    -88.19
REMARK 500    CYS A 125      126.56    -39.41
REMARK 500    SER A 294     -144.29     52.02
REMARK 500    TRP A 299       60.00   -161.84
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 A1623        DISTANCE =  5.66 ANGSTROMS
REMARK 525    HOH A1654        DISTANCE =  6.36 ANGSTROMS
REMARK 525    HOH A1681        DISTANCE =  6.47 ANGSTROMS
REMARK 525    HOH A1682        DISTANCE =  5.35 ANGSTROMS
REMARK 525    HOH A1687        DISTANCE =  6.10 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620  (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620  SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 500  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A  92   OD1
REMARK 620 2 ASP A 149   OD2  82.0
REMARK 620 3 ASP A 139   OD2 164.7  82.8
REMARK 620 4 ALA A 142   O    92.3  82.9  83.7
REMARK 620 5 GLY A 184   O    78.5 152.5 115.0  78.7
REMARK 620 6 HOH A 630   O    82.7  93.3 100.3 174.1 103.2
REMARK 620 7 ASP A 139   OD1 145.1 131.0  50.1 101.9  73.3  84.1
REMARK 620 N                    1     2     3     4     5     6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 501  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 112   O
REMARK 620 2 ASP A 118   OD2 163.3
REMARK 620 3 ASP A 118   OD1 139.3  52.1
REMARK 620 4 ASP A 114   O    83.3  81.2 105.4
REMARK 620 5 GLU A 109   OE1 113.2  80.0  73.9 156.1
REMARK 620 6 HOH A 604   O    73.2 109.4  69.9  78.8 121.5
REMARK 620 7 GLU A 109   OE2  74.7 121.8  84.2 154.6  48.8  82.9
REMARK 620 8 HOH A 656   O    78.6  90.8 142.1  71.6  94.1 141.0 115.1
REMARK 620 N                    1     2     3     4     5     6     7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A 502  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 147   O
REMARK 620 2 ASP A 143   OD2 149.4
REMARK 620 3 ASP A 143   OD1 158.6  46.7
REMARK 620 4 PHE A 144   O    77.4  74.0 107.9
REMARK 620 5 HOH A 788   O    93.2  78.7 106.7  95.0
REMARK 620 6 ASP A 128   OD2  95.2 112.7  79.8 172.3  83.2
REMARK 620 7 ASP A 149   OD1  89.3  96.7  71.7  80.7 174.4 101.6
REMARK 620 N                    1     2     3     4     5     6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAF A 2000
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 2001
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAF A 3000
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 3001
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 3002
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAF A 4000
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 4001
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 500
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 501
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 502
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1HT6   RELATED DB: PDB
REMARK 900 BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) IN ITS NATIVE STATE
REMARK 900 RELATED ID: 1P6W   RELATED DB: PDB
REMARK 900 BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) IN COMPLEX WITH
REMARK 900 SUBSTRATE ANALOGUE METHYL 4I,4II,4III-TRI-
REMARK 900 THIOMALTOTETRAOSIDE (THIO-DP4)
REMARK 900 RELATED ID: 1RP8   RELATED DB: PDB
REMARK 900 BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) INACTIVE MUTANT D180A
REMARK 900 IN COMPLEX WITH MALTOHEPTAOSE
REMARK 900 RELATED ID: 1RP9   RELATED DB: PDB
REMARK 900 BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) INACTIVE MUTANT D180A
REMARK 900 IN COMPLEX WITH ACARBOSE
REMARK 900 RELATED ID: 1AMY   RELATED DB: PDB
REMARK 900 BARLEY ALPHA-AMYLASE ISOZYME 2 (AMY2) IN ITS NATIVE STATE
REMARK 900 RELATED ID: 1BG9   RELATED DB: PDB
REMARK 900 BARLEY ALPHA-AMYLASE ISOZYME 2 (AMY2) IN COMPLEX WITH
REMARK 900 ACARBOSE
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 ACCORDING TO THE AUTHORS, THERE IS AN ERROR IN SWISSPROT
REMARK 999 DATABASE, CORRECTED BY EXAMINATION OF THE CRYSTAL
REMARK 999 STRUCTURE.
DBREF  1RPK A    1   405  UNP    P00693   AMY1_HORVU      25    429
SEQADV 1RPK VAL A  284  UNP  P00693    ALA   308 SEE REMARK 999
SEQRES   1 A  405  HIS GLN VAL LEU PHE GLN GLY PHE ASN TRP GLU SER TRP
SEQRES   2 A  405  LYS GLN SER GLY GLY TRP TYR ASN MET MET MET GLY LYS
SEQRES   3 A  405  VAL ASP ASP ILE ALA ALA ALA GLY VAL THR HIS VAL TRP
SEQRES   4 A  405  LEU PRO PRO PRO SER HIS SER VAL SER ASN GLU GLY TYR
SEQRES   5 A  405  MET PRO GLY ARG LEU TYR ASP ILE ASP ALA SER LYS TYR
SEQRES   6 A  405  GLY ASN ALA ALA GLU LEU LYS SER LEU ILE GLY ALA LEU
SEQRES   7 A  405  HIS GLY LYS GLY VAL GLN ALA ILE ALA ASP ILE VAL ILE
SEQRES   8 A  405  ASN HIS ARG CYS ALA ASP TYR LYS ASP SER ARG GLY ILE
SEQRES   9 A  405  TYR CYS ILE PHE GLU GLY GLY THR SER ASP GLY ARG LEU
SEQRES  10 A  405  ASP TRP GLY PRO HIS MET ILE CYS ARG ASP ASP THR LYS
SEQRES  11 A  405  TYR SER ASP GLY THR ALA ASN LEU ASP THR GLY ALA ASP
SEQRES  12 A  405  PHE ALA ALA ALA PRO ASP ILE ASP HIS LEU ASN ASP ARG
SEQRES  13 A  405  VAL GLN ARG GLU LEU LYS GLU TRP LEU LEU TRP LEU LYS
SEQRES  14 A  405  SER ASP LEU GLY PHE ASP ALA TRP ARG LEU ASP PHE ALA
SEQRES  15 A  405  ARG GLY TYR SER PRO GLU MET ALA LYS VAL TYR ILE ASP
SEQRES  16 A  405  GLY THR SER PRO SER LEU ALA VAL ALA GLU VAL TRP ASP
SEQRES  17 A  405  ASN MET ALA THR GLY GLY ASP GLY LYS PRO ASN TYR ASP
SEQRES  18 A  405  GLN ASP ALA HIS ARG GLN ASN LEU VAL ASN TRP VAL ASP
SEQRES  19 A  405  LYS VAL GLY GLY ALA ALA SER ALA GLY MET VAL PHE ASP
SEQRES  20 A  405  PHE THR THR LYS GLY ILE LEU ASN ALA ALA VAL GLU GLY
SEQRES  21 A  405  GLU LEU TRP ARG LEU ILE ASP PRO GLN GLY LYS ALA PRO
SEQRES  22 A  405  GLY VAL MET GLY TRP TRP PRO ALA LYS ALA VAL THR PHE
SEQRES  23 A  405  VAL ASP ASN HIS ASP THR GLY SER THR GLN ALA MET TRP
SEQRES  24 A  405  PRO PHE PRO SER ASP LYS VAL MET GLN GLY TYR ALA TYR
SEQRES  25 A  405  ILE LEU THR HIS PRO GLY ILE PRO CYS ILE PHE TYR ASP
SEQRES  26 A  405  HIS PHE PHE ASN TRP GLY PHE LYS ASP GLN ILE ALA ALA
SEQRES  27 A  405  LEU VAL ALA ILE ARG LYS ARG ASN GLY ILE THR ALA THR
SEQRES  28 A  405  SER ALA LEU LYS ILE LEU MET HIS GLU GLY ASP ALA TYR
SEQRES  29 A  405  VAL ALA GLU ILE ASP GLY LYS VAL VAL VAL LYS ILE GLY
SEQRES  30 A  405  SER ARG TYR ASP VAL GLY ALA VAL ILE PRO ALA GLY PHE
SEQRES  31 A  405  VAL THR SER ALA HIS GLY ASN ASP TYR ALA VAL TRP GLU
SEQRES  32 A  405  LYS ASN
HET    DAF  A2000      21
HET    GLC  A2001      12
HET    DAF  A3000      21
HET    GLC  A3001      11
HET    GLC  A3002      12
HET    DAF  A4000      21
HET    GLC  A4001      12
HET     CA  A 500       1
HET     CA  A 501       1
HET     CA  A 502       1
HETNAM     DAF 1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-
HETNAM   2 DAF  TRIHYDROXYCYCLOHEX-5-ENYL)AMINO)FRUCTOSE
HETNAM     GLC ALPHA-D-GLUCOSE
HETNAM      CA CALCIUM ION
FORMUL   2  DAF    3(C13 H23 N O7)
FORMUL   2  GLC    4(C6 H12 O6)
FORMUL   5   CA    3(CA 2+)
FORMUL   8  HOH   *549(H2 O)
HELIX    1   1 GLU A   11  GLN A   15  5                                   5
HELIX    2   2 GLY A   18  MET A   24  1                                   7
HELIX    3   3 LYS A   26  ALA A   33  1                                   8
HELIX    4   4 ASP A   59  SER A   63  5                                   5
HELIX    5   5 ASN A   67  LYS A   81  1                                  15
HELIX    6   6 GLY A  120  ILE A  124  5                                   5
HELIX    7   7 ASN A  154  ASP A  171  1                                  18
HELIX    8   8 PHE A  181  TYR A  185  5                                   5
HELIX    9   9 SER A  186  SER A  198  1                                  13
HELIX   10  10 GLN A  222  GLY A  237  1                                  16
HELIX   11  11 GLY A  238  SER A  241  5                                   4
HELIX   12  12 ASP A  247  VAL A  258  1                                  12
HELIX   13  13 GLU A  261  ILE A  266  5                                   6
HELIX   14  14 GLY A  274  TRP A  278  5                                   5
HELIX   15  15 TRP A  279  ALA A  281  5                                   3
HELIX   16  16 PRO A  302  ASP A  304  5                                   3
HELIX   17  17 LYS A  305  HIS A  316  1                                  12
HELIX   18  18 TYR A  324  ASN A  329  1                                   6
HELIX   19  19 PHE A  332  ASN A  346  1                                  15
HELIX   20  20 VAL A  382  ILE A  386  5                                   5
SHEET    1   A 9 LEU A   4  GLN A   6  0
SHEET    2   A 9 HIS A  37  LEU A  40  1  O  TRP A  39   N  PHE A   5
SHEET    3   A 9 GLN A  84  ILE A  89  1  O  ILE A  86   N  VAL A  38
SHEET    4   A 9 ALA A 176  LEU A 179  1  O  ALA A 176   N  ALA A  87
SHEET    5   A 9 ALA A 202  ALA A 204  1  O  VAL A 203   N  TRP A 177
SHEET    6   A 9 GLY A 243  PHE A 246  1  O  MET A 244   N  ALA A 204
SHEET    7   A 9 ALA A 283  PHE A 286  1  O  VAL A 284   N  VAL A 245
SHEET    8   A 9 ILE A 319  PHE A 323  1  O  CYS A 321   N  THR A 285
SHEET    9   A 9 LEU A   4  GLN A   6  1  N  GLN A   6   O  ILE A 322
SHEET    1   B 2 TYR A  98  LYS A  99  0
SHEET    2   B 2 TYR A 105  ILE A 107 -1  O  ILE A 107   N  TYR A  98
SHEET    1   C 5 LEU A 354  GLU A 360  0
SHEET    2   C 5 ALA A 363  ILE A 368 -1  O  GLU A 367   N  LYS A 355
SHEET    3   C 5 VAL A 372  ILE A 376 -1  O  VAL A 372   N  ILE A 368
SHEET    4   C 5 TYR A 399  GLU A 403 -1  O  TRP A 402   N  VAL A 373
SHEET    5   C 5 VAL A 391  GLY A 396 -1  N  ALA A 394   O  VAL A 401
LINK         C1  DAF A2000                 O4  GLC A2001     1555   1555  1.40
LINK         C1  DAF A3000                 O4  GLC A3001     1555   1555  1.40
LINK         C1  GLC A3001                 O4  GLC A3002     1555   1555  1.40
LINK         C1  DAF A4000                 O4  GLC A4001     1555   1555  1.40
LINK        CA    CA A 500                 OD1 ASN A  92     1555   1555  2.45
LINK        CA    CA A 500                 OD2 ASP A 149     1555   1555  2.37
LINK        CA    CA A 500                 OD2 ASP A 139     1555   1555  2.38
LINK        CA    CA A 500                 O   ALA A 142     1555   1555  2.50
LINK        CA    CA A 500                 O   GLY A 184     1555   1555  2.38
LINK        CA    CA A 500                 O   HOH A 630     1555   1555  2.44
LINK        CA    CA A 500                 OD1 ASP A 139     1555   1555  2.72
LINK        CA    CA A 501                 O   THR A 112     1555   1555  2.61
LINK        CA    CA A 501                 OD2 ASP A 118     1555   1555  2.36
LINK        CA    CA A 501                 OD1 ASP A 118     1555   1555  2.63
LINK        CA    CA A 501                 O   ASP A 114     1555   1555  2.32
LINK        CA    CA A 501                 OE1 GLU A 109     1555   1555  2.73
LINK        CA    CA A 501                 O   HOH A 604     1555   1555  2.50
LINK        CA    CA A 501                 OE2 GLU A 109     1555   1555  2.54
LINK        CA    CA A 501                 O   HOH A 656     1555   1555  2.33
LINK        CA    CA A 502                 O   ALA A 147     1555   1555  2.35
LINK        CA    CA A 502                 OD2 ASP A 143     1555   1555  2.98
LINK        CA    CA A 502                 OD1 ASP A 143     1555   1555  2.42
LINK        CA    CA A 502                 O   PHE A 144     1555   1555  2.25
LINK        CA    CA A 502                 O   HOH A 788     1555   1555  2.42
LINK        CA    CA A 502                 OD2 ASP A 128     1555   1555  2.27
LINK        CA    CA A 502                 OD1 ASP A 149     1555   1555  2.37
SITE     1 AC1 15 TYR A  52  HIS A  93  PHE A 144  ARG A 178
SITE     2 AC1 15 ASP A 180  PHE A 181  ARG A 183  GLU A 205
SITE     3 AC1 15 TRP A 207  HIS A 290  ASP A 291  MET A 298
SITE     4 AC1 15 HOH A 676  HOH A1675  GLC A2001
SITE     1 AC2  6 ARG A 183  TRP A 207  ASP A 208  ASN A 209
SITE     2 AC2  6 MET A 298  DAF A2000
SITE     1 AC3 15 LYS A 375  TYR A 380  ASP A 381  VAL A 382
SITE     2 AC3 15 GLY A 383  THR A 392  HIS A 395  GLY A 396
SITE     3 AC3 15 ASP A 398  TYR A 399  TRP A 402  HOH A1096
SITE     4 AC3 15 HOH A1540  HOH A1653  GLC A3001
SITE     1 AC4  9 TYR A 380  HIS A 395  GLY A 396  ASP A 398
SITE     2 AC4  9 HOH A 904  HOH A1342  HOH A1602  DAF A3000
SITE     3 AC4  9 GLC A3002
SITE     1 AC5  4 ALA A 240  HOH A1539  HOH A1602  GLC A3001
SITE     1 AC6 10 VAL A 230  ASP A 234  TRP A 278  TRP A 279
SITE     2 AC6 10 HOH A 865  HOH A1542  HOH A1543  HOH A1547
SITE     3 AC6 10 HOH A1548  GLC A4001
SITE     1 AC7  8 GLN A 227  VAL A 230  TRP A 278  HOH A1059
SITE     2 AC7  8 HOH A1550  HOH A1551  HOH A1605  DAF A4000
SITE     1 AC8  6 ASN A  92  ASP A 139  ALA A 142  ASP A 149
SITE     2 AC8  6 GLY A 184  HOH A 630
SITE     1 AC9  6 GLU A 109  THR A 112  ASP A 114  ASP A 118
SITE     2 AC9  6 HOH A 604  HOH A 656
SITE     1 BC1  6 ASP A 128  ASP A 143  PHE A 144  ALA A 147
SITE     2 BC1  6 ASP A 149  HOH A 788
CRYST1   93.390   72.920   61.390  90.00  90.00  90.00 P 21 21 2     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      0.010708  0.000000  0.000000        0.00000
SCALE2      0.000000  0.013714  0.000000        0.00000
SCALE3      0.000000  0.000000  0.016289        0.00000
      
PROCHECK
Go to PROCHECK summary
 References