spacer
spacer

PDBsum entry 2ags

Go to PDB code: 
Top Page protein ligands links
Hydrolase PDB id
2ags
Jmol
Contents
Protein chain
634 a.a.
Ligands
SO4 ×2
FKD
Waters ×805
HEADER    HYDROLASE                               27-JUL-05   2AGS
TITLE     TRYPANOSOMA RANGELI SIALIDASE IN COMPLEX WITH 2-KETO-3-
TITLE    2 DEOXY-D-GLYCERO-D-GALACTO-2,3-DIFLUORO-NONONIC ACID (2,3-
TITLE    3 DIFLUORO-KDN)
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: SIALIDASE;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: RESIDUES 23-660;
COMPND   5 EC: 3.2.1.18;
COMPND   6 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: TRYPANOSOMA RANGELI;
SOURCE   3 ORGANISM_TAXID: 5698;
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   6 EXPRESSION_SYSTEM_STRAIN: TOP10;
SOURCE   7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PTRCHISA
KEYWDS    BETA-PROPELLER, COVALENT ENZYME-INTERMEDIATE COMPLEX, BETA-
KEYWDS   2 SANDWICH, HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.F.AMAYA,P.M.ALZARI,A.BUSCHIAZZO
REVDAT   4   24-FEB-09 2AGS    1       VERSN
REVDAT   3   28-FEB-06 2AGS    1       JRNL
REVDAT   2   17-JAN-06 2AGS    1       AUTHOR JRNL   SEQADV
REVDAT   1   22-NOV-05 2AGS    0
JRNL        AUTH   A.G.WATTS,P.OPPEZZO,S.G.WITHERS,P.M.ALZARI,
JRNL        AUTH 2 A.BUSCHIAZZO
JRNL        TITL   STRUCTURAL AND KINETIC ANALYSIS OF TWO COVALENT
JRNL        TITL 2 SIALOSYL-ENZYME INTERMEDIATES ON TRYPANOSOMA
JRNL        TITL 3 RANGELI SIALIDASE.
JRNL        REF    J.BIOL.CHEM.                  V. 281  4149 2006
JRNL        REFN                   ISSN 0021-9258
JRNL        PMID   16298994
JRNL        DOI    10.1074/JBC.M510677200
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    1.70 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0005
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 35.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 98.3
REMARK   3   NUMBER OF REFLECTIONS             : 81306
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 + TEST SET) : 0.154
REMARK   3   R VALUE            (WORKING SET) : 0.154
REMARK   3   FREE R VALUE                     : 0.189
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000
REMARK   3   FREE R VALUE TEST SET COUNT      : 4074
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 20
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.70
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.74
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 5242
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 91.77
REMARK   3   BIN R VALUE           (WORKING SET) : 0.1850
REMARK   3   BIN FREE R VALUE SET COUNT          : 287
REMARK   3   BIN FREE R VALUE                    : 0.2300
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 4934
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 28
REMARK   3   SOLVENT ATOMS            : 805
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 12.83
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 0.72000
REMARK   3    B22 (A**2) : -0.34000
REMARK   3    B33 (A**2) : -0.38000
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 OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): 0.088
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.090
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.055
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.620
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.962
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.947
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  5077 ; 0.017 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  4551 ; 0.002 ; 0.020
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  6913 ; 1.673 ; 1.948
REMARK   3   BOND ANGLES OTHERS          (DEGREES): 10567 ; 0.829 ; 3.000
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   645 ; 7.247 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   221 ;32.627 ;23.575
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   822 ;11.818 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    37 ;13.230 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   768 ; 0.101 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  5724 ; 0.007 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  1054 ; 0.001 ; 0.020
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1086 ; 0.208 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  5250 ; 0.201 ; 0.200
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2666 ; 0.184 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  3353 ; 0.088 ; 0.200
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   733 ; 0.155 ; 0.200
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    13 ; 0.083 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):    56 ; 0.223 ; 0.200
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    28 ; 0.136 ; 0.200
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  3978 ; 1.335 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  1316 ; 0.288 ; 1.500
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  5122 ; 1.580 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  2218 ; 2.554 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1790 ; 3.527 ; 4.500
REMARK   3
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  NCS RESTRAINTS STATISTICS
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : BABINET MODEL WITH MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.20
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK   3  RIDING POSITIONS
REMARK   4
REMARK   4 2AGS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-05.
REMARK 100 THE RCSB ID CODE IS RCSB033875.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 14-FEB-05
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 6.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : ID14-2
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.933
REMARK 200  MONOCHROMATOR                  : DIAMOND (111), GE(220)
REMARK 200  OPTICS                         : TOROIDAL MIRROR
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 4
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 81374
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.700
REMARK 200  RESOLUTION RANGE LOW       (A) : 35.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.5
REMARK 200  DATA REDUNDANCY                : 3.400
REMARK 200  R MERGE                    (I) : 0.06600
REMARK 200  R SYM                      (I) : 0.06600
REMARK 200   FOR THE DATA SET  : 8.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.79
REMARK 200  COMPLETENESS FOR SHELL     (%) : 93.8
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.90
REMARK 200  R MERGE FOR SHELL          (I) : 0.24700
REMARK 200  R SYM FOR SHELL            (I) : 0.24700
REMARK 200   FOR SHELL         : 2.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 2A75
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 53.40
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM SULFATE, SODIUM
REMARK 280  CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280  291K
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       36.83600
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       52.90800
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       47.78450
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       52.90800
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       36.83600
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       47.78450
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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER
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     MET A   -13
REMARK 465     GLY A   -12
REMARK 465     GLY A   -11
REMARK 465     SER A   -10
REMARK 465     HIS A    -9
REMARK 465     HIS A    -8
REMARK 465     HIS A    -7
REMARK 465     HIS A    -6
REMARK 465     HIS A    -5
REMARK 465     HIS A    -4
REMARK 465     GLY A    -3
REMARK 465     GLY A   632
REMARK 465     GLY A   633
REMARK 465     ALA A   634
REMARK 465     GLY A   635
REMARK 465     THR A   636
REMARK 465     ALA A   637
REMARK 465     ALA A   638
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     MET A  -2    CB   CG   SD   CE
REMARK 470     ALA A  -1    CB
REMARK 470     PRO A 406    CG   CD
REMARK 470     SER A 407    OG
REMARK 470     LYS A 408    CG   CD   CE   NZ
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   O    HOH A  1054     O    HOH A  1646              2.16
REMARK 500
REMARK 500 REMARK: NULL
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    ASP A  52   CB  -  CG  -  OD1 ANGL. DEV. =   5.8 DEGREES
REMARK 500    ARG A 251   NE  -  CZ  -  NH1 ANGL. DEV. =  -5.1 DEGREES
REMARK 500    ARG A 251   NE  -  CZ  -  NH2 ANGL. DEV. =   5.2 DEGREES
REMARK 500    ARG A 317   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 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    ALA A  -1      115.18     47.68
REMARK 500    ASN A  15      -65.05   -161.25
REMARK 500    ILE A  37       60.49     61.74
REMARK 500    ASN A  61       67.30   -103.11
REMARK 500    LYS A 116       -2.86   -146.88
REMARK 500    ASN A 145       46.36     34.03
REMARK 500    VAL A 180      132.95     85.74
REMARK 500    ALA A 183     -163.56   -104.58
REMARK 500    GLU A 231       60.50     31.43
REMARK 500    THR A 270      -78.18   -141.01
REMARK 500    SER A 278      169.81    179.47
REMARK 500    ARG A 312     -142.31     58.64
REMARK 500    ARG A 317       69.16     67.50
REMARK 500    GLN A 326      -67.00   -133.57
REMARK 500    SER A 341     -126.13   -107.04
REMARK 500    PRO A 406       50.53     -3.62
REMARK 500    SER A 407     -136.28    -76.29
REMARK 500    SER A 425     -129.30   -141.29
REMARK 500    ASN A 429     -158.26   -134.85
REMARK 500    VAL A 467      -93.00   -114.21
REMARK 500    ASP A 511       46.55   -143.71
REMARK 500    HIS A 543       -8.96     74.33
REMARK 500    ASN A 610       32.02    -92.45
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500                                 MODEL     OMEGA
REMARK 500 MET A   -2     ALA A   -1                 -136.46
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 A1522        DISTANCE =  5.10 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 901
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FKD A 700
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1N1S   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF TRYPANOSOMA RANGELI SIALIDASE
REMARK 900 RELATED ID: 2A75   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF TRYPANOSOMA RANGELI SIALIDASE IN
REMARK 900 COMPLEX WITH 2,3-DIFLUOROSIALIC ACID (COVALENT INTERMEDIATE)
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 AUTHORS INDICATE THAT THE AMINOACID SEQUENCE IN THE
REMARK 999 SEQUENCE DATABASE IS INCORRECT
DBREF  2AGS A    1   638  UNP    O44049   O44049_TRYRA    23    660
SEQADV 2AGS MET A  -13  UNP  O44049              CLONING ARTIFACT
SEQADV 2AGS GLY A  -12  UNP  O44049              CLONING ARTIFACT
SEQADV 2AGS GLY A  -11  UNP  O44049              CLONING ARTIFACT
SEQADV 2AGS SER A  -10  UNP  O44049              CLONING ARTIFACT
SEQADV 2AGS HIS A   -9  UNP  O44049              EXPRESSION TAG
SEQADV 2AGS HIS A   -8  UNP  O44049              EXPRESSION TAG
SEQADV 2AGS HIS A   -7  UNP  O44049              EXPRESSION TAG
SEQADV 2AGS HIS A   -6  UNP  O44049              EXPRESSION TAG
SEQADV 2AGS HIS A   -5  UNP  O44049              EXPRESSION TAG
SEQADV 2AGS HIS A   -4  UNP  O44049              EXPRESSION TAG
SEQADV 2AGS GLY A   -3  UNP  O44049              CLONING ARTIFACT
SEQADV 2AGS MET A   -2  UNP  O44049              CLONING ARTIFACT
SEQADV 2AGS ALA A   -1  UNP  O44049              CLONING ARTIFACT
SEQADV 2AGS SER A    0  UNP  O44049              CLONING ARTIFACT
SEQADV 2AGS ILE A   50  UNP  O44049    THR    72 SEE REMARK 999
SEQADV 2AGS ALA A  186  UNP  O44049    GLY   208 SEE REMARK 999
SEQADV 2AGS LEU A  372  UNP  O44049    PHE   394 SEE REMARK 999
SEQADV 2AGS VAL A  606  UNP  O44049    ILE   628 SEE REMARK 999
SEQRES   1 A  652  MET GLY GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA
SEQRES   2 A  652  SER LEU ALA PRO GLY SER SER ARG VAL GLU LEU PHE LYS
SEQRES   3 A  652  ARG LYS ASN SER THR VAL PRO PHE GLU GLU SER ASN GLY
SEQRES   4 A  652  THR ILE ARG GLU ARG VAL VAL HIS SER PHE ARG ILE PRO
SEQRES   5 A  652  THR ILE VAL ASN VAL ASP GLY VAL MET VAL ALA ILE ALA
SEQRES   6 A  652  ASP ALA ARG TYR GLU THR SER PHE ASP ASN SER PHE ILE
SEQRES   7 A  652  GLU THR ALA VAL LYS TYR SER VAL ASP ASP GLY ALA THR
SEQRES   8 A  652  TRP ASN THR GLN ILE ALA ILE LYS ASN SER ARG ALA SER
SEQRES   9 A  652  SER VAL SER ARG VAL MET ASP ALA THR VAL ILE VAL LYS
SEQRES  10 A  652  GLY ASN LYS LEU TYR ILE LEU VAL GLY SER PHE ASN LYS
SEQRES  11 A  652  THR ARG ASN SER TRP THR GLN HIS ARG ASP GLY SER ASP
SEQRES  12 A  652  TRP GLU PRO LEU LEU VAL VAL GLY GLU VAL THR LYS SER
SEQRES  13 A  652  ALA ALA ASN GLY LYS THR THR ALA THR ILE SER TRP GLY
SEQRES  14 A  652  LYS PRO VAL SER LEU LYS PRO LEU PHE PRO ALA GLU PHE
SEQRES  15 A  652  ASP GLY ILE LEU THR LYS GLU PHE ILE GLY GLY VAL GLY
SEQRES  16 A  652  ALA ALA ILE VAL ALA SER ASN GLY ASN LEU VAL TYR PRO
SEQRES  17 A  652  VAL GLN ILE ALA ASP MET GLY GLY ARG VAL PHE THR LYS
SEQRES  18 A  652  ILE MET TYR SER GLU ASP ASP GLY ASN THR TRP LYS PHE
SEQRES  19 A  652  ALA GLU GLY ARG SER LYS PHE GLY CYS SER GLU PRO ALA
SEQRES  20 A  652  VAL LEU GLU TRP GLU GLY LYS LEU ILE ILE ASN ASN ARG
SEQRES  21 A  652  VAL ASP GLY ASN ARG ARG LEU VAL TYR GLU SER SER ASP
SEQRES  22 A  652  MET GLY LYS THR TRP VAL GLU ALA LEU GLY THR LEU SER
SEQRES  23 A  652  HIS VAL TRP THR ASN SER PRO THR SER ASN GLN GLN ASP
SEQRES  24 A  652  CYS GLN SER SER PHE VAL ALA VAL THR ILE GLU GLY LYS
SEQRES  25 A  652  ARG VAL MET LEU PHE THR HIS PRO LEU ASN LEU LYS GLY
SEQRES  26 A  652  ARG TRP MET ARG ASP ARG LEU HIS LEU TRP MET THR ASP
SEQRES  27 A  652  ASN GLN ARG ILE PHE ASP VAL GLY GLN ILE SER ILE GLY
SEQRES  28 A  652  ASP GLU ASN SER GLY TYR SER SER VAL LEU TYR LYS ASP
SEQRES  29 A  652  ASP LYS LEU TYR SER LEU HIS GLU ILE ASN THR ASN ASP
SEQRES  30 A  652  VAL TYR SER LEU VAL PHE VAL ARG LEU ILE GLY GLU LEU
SEQRES  31 A  652  GLN LEU MET LYS SER VAL VAL ARG THR TRP LYS GLU GLU
SEQRES  32 A  652  ASP ASN HIS LEU ALA SER ILE CYS THR PRO VAL VAL PRO
SEQRES  33 A  652  ALA THR PRO PRO SER LYS GLY GLY CYS GLY ALA ALA VAL
SEQRES  34 A  652  PRO THR ALA GLY LEU VAL GLY PHE LEU SER HIS SER ALA
SEQRES  35 A  652  ASN GLY SER VAL TRP GLU ASP VAL TYR ARG CYS VAL ASP
SEQRES  36 A  652  ALA ASN VAL ALA ASN ALA GLU ARG VAL PRO ASN GLY LEU
SEQRES  37 A  652  LYS PHE ASN GLY VAL GLY GLY GLY ALA VAL TRP PRO VAL
SEQRES  38 A  652  ALA ARG GLN GLY GLN THR ARG ARG TYR GLN PHE ALA ASN
SEQRES  39 A  652  TYR ARG PHE THR LEU VAL ALA THR VAL THR ILE ASP GLU
SEQRES  40 A  652  LEU PRO LYS GLY THR SER PRO LEU LEU GLY ALA GLY LEU
SEQRES  41 A  652  GLU GLY PRO GLY ASP ALA LYS LEU LEU GLY LEU SER TYR
SEQRES  42 A  652  ASP LYS ASN ARG GLN TRP ARG PRO LEU TYR GLY ALA ALA
SEQRES  43 A  652  PRO ALA SER PRO THR GLY SER TRP GLU LEU HIS LYS LYS
SEQRES  44 A  652  TYR HIS VAL VAL LEU THR MET ALA ASP ARG GLN GLY SER
SEQRES  45 A  652  VAL TYR VAL ASP GLY GLN PRO LEU ALA GLY SER GLY ASN
SEQRES  46 A  652  THR VAL VAL ARG GLY ALA THR LEU PRO ASP ILE SER HIS
SEQRES  47 A  652  PHE TYR ILE GLY GLY PRO ARG SER LYS GLY ALA PRO THR
SEQRES  48 A  652  ASP SER ARG VAL THR VAL THR ASN VAL VAL LEU TYR ASN
SEQRES  49 A  652  ARG ARG LEU ASN SER SER GLU ILE ARG THR LEU PHE LEU
SEQRES  50 A  652  SER GLN ASP MET ILE GLY THR ASP GLY GLY ALA GLY THR
SEQRES  51 A  652  ALA ALA
HET    SO4  A 901       5
HET    SO4  A 902       5
HET    FKD  A 700      18
HETNAM     SO4 SULFATE ION
HETNAM     FKD 2,6-ANHYDRO-3-DEOXY-3-FLUORO-L-ARABINO-D-GALACTO-
HETNAM   2 FKD  NONONIC ACID
HETSYN     FKD 2-KETO-3-DEOXY-D-GLYCERO-D-GALACTO-3-FLUORONONONIC
HETSYN   2 FKD  ACID; 2,6-ANHYDRO-3-DEOXY-3-FLUORONONONIC ACID
FORMUL   2  SO4    2(O4 S 2-)
FORMUL   4  FKD    C9 H15 F O8
FORMUL   5  HOH   *805(H2 O)
HELIX    1   1 SER A  120  HIS A  124  5                                   5
HELIX    2   2 LYS A  161  PHE A  164  5                                   4
HELIX    3   3 LEU A  372  ILE A  396  1                                  25
HELIX    4   4 ALA A  468  GLY A  471  5                                   4
HELIX    5   5 TYR A  476  ASN A  480  5                                   5
HELIX    6   6 ASN A  614  SER A  624  1                                  11
SHEET    1   A 4 SER A   6  PHE A  11  0
SHEET    2   A 4 VAL A 364  ARG A 371 -1  O  ARG A 371   N  SER A   6
SHEET    3   A 4 LYS A 352  THR A 361 -1  N  SER A 355   O  VAL A 370
SHEET    4   A 4 SER A 344  LYS A 349 -1  N  LEU A 347   O  TYR A 354
SHEET    1   B 2 THR A  17  GLU A  21  0
SHEET    2   B 2 ILE A  27  VAL A  31 -1  O  ARG A  28   N  PHE A  20
SHEET    1   C 4 SER A  34  VAL A  43  0
SHEET    2   C 4 VAL A  46  ARG A  54 -1  O  ILE A  50   N  THR A  39
SHEET    3   C 4 ILE A  64  SER A  71 -1  O  LYS A  69   N  ALA A  49
SHEET    4   C 4 ASN A  79  ILE A  84 -1  O  GLN A  81   N  VAL A  68
SHEET    1   D 3 LYS A 147  TRP A 154  0
SHEET    2   D 3 TRP A 130  ALA A 144 -1  N  GLU A 138   O  SER A 153
SHEET    3   D 3 VAL A 158  SER A 159 -1  O  VAL A 158   N  LEU A 134
SHEET    1   E 5 LYS A 147  TRP A 154  0
SHEET    2   E 5 TRP A 130  ALA A 144 -1  N  GLU A 138   O  SER A 153
SHEET    3   E 5 LYS A 106  PHE A 114 -1  N  ILE A 109   O  VAL A 135
SHEET    4   E 5 ARG A  94  LYS A 103 -1  N  ILE A 101   O  TYR A 108
SHEET    5   E 5 GLY A 181  ALA A 182  1  O  GLY A 181   N  ALA A  98
SHEET    1   F 4 GLU A 167  PHE A 168  0
SHEET    2   F 4 ILE A 171  GLY A 178 -1  O  ILE A 171   N  PHE A 168
SHEET    3   F 4 LEU A 191  ASP A 199 -1  O  GLN A 196   N  ILE A 177
SHEET    4   F 4 ILE A 184  VAL A 185 -1  N  ILE A 184   O  VAL A 192
SHEET    1   G 5 GLU A 167  PHE A 168  0
SHEET    2   G 5 ILE A 171  GLY A 178 -1  O  ILE A 171   N  PHE A 168
SHEET    3   G 5 LEU A 191  ASP A 199 -1  O  GLN A 196   N  ILE A 177
SHEET    4   G 5 VAL A 204  SER A 211 -1  O  PHE A 205   N  ILE A 197
SHEET    5   G 5 LYS A 219  PHE A 220 -1  O  LYS A 219   N  TYR A 210
SHEET    1   H 4 CYS A 229  TRP A 237  0
SHEET    2   H 4 LYS A 240  VAL A 247 -1  O  LYS A 240   N  TRP A 237
SHEET    3   H 4 VAL A 254  SER A 257 -1  O  TYR A 255   N  ILE A 243
SHEET    4   H 4 VAL A 265  GLU A 266 -1  O  VAL A 265   N  GLU A 256
SHEET    1   I 4 PHE A 290  ILE A 295  0
SHEET    2   I 4 LYS A 298  PRO A 306 -1  O  LEU A 302   N  VAL A 291
SHEET    3   I 4 LEU A 318  THR A 323 -1  O  THR A 323   N  MET A 301
SHEET    4   I 4 ILE A 328  GLN A 333 -1  O  PHE A 329   N  MET A 322
SHEET    1   J 7 ALA A 447  VAL A 450  0
SHEET    2   J 7 GLY A 453  PHE A 456 -1  O  LYS A 455   N  GLU A 448
SHEET    3   J 7 VAL A 601  TYR A 609 -1  O  VAL A 601   N  PHE A 456
SHEET    4   J 7 ARG A 482  ILE A 491 -1  N  THR A 488   O  THR A 604
SHEET    5   J 7 TYR A 546  ALA A 553 -1  O  VAL A 548   N  ALA A 487
SHEET    6   J 7 GLN A 556  VAL A 561 -1  O  TYR A 560   N  VAL A 549
SHEET    7   J 7 GLN A 564  PRO A 565 -1  O  GLN A 564   N  VAL A 561
SHEET    1   K13 TRP A 525  TYR A 529  0
SHEET    2   K13 LYS A 513  ASP A 520 -1  N  GLY A 516   O  LEU A 528
SHEET    3   K13 THR A 498  LEU A 506 -1  N  LEU A 502   O  LEU A 517
SHEET    4   K13 ILE A 582  GLY A 588 -1  O  GLY A 588   N  LEU A 501
SHEET    5   K13 GLY A 462  PRO A 466 -1  N  TRP A 465   O  PHE A 585
SHEET    6   K13 ALA A 442  ALA A 445 -1  N  ASN A 443   O  VAL A 464
SHEET    7   K13 VAL A 432  ASP A 435 -1  N  TRP A 433   O  ALA A 442
SHEET    8   K13 LEU A 420  ALA A 428 -1  N  SER A 427   O  GLU A 434
SHEET    9   K13 VAL A 601  TYR A 609 -1  O  VAL A 606   N  LEU A 424
SHEET   10   K13 ARG A 482  ILE A 491 -1  N  THR A 488   O  THR A 604
SHEET   11   K13 TYR A 546  ALA A 553 -1  O  VAL A 548   N  ALA A 487
SHEET   12   K13 GLN A 556  VAL A 561 -1  O  TYR A 560   N  VAL A 549
SHEET   13   K13 ASN A 571  THR A 572 -1  O  ASN A 571   N  GLY A 557
SSBOND   1 CYS A  397    CYS A  411                          1555   1555  2.05
LINK         OH  TYR A 343                 C2  FKD A 700     1555   1555  1.43
SITE     1 AC1  9 ARG A 469  ARG A 591  SER A 592  LYS A 593
SITE     2 AC1  9 HOH A1440  HOH A1514  HOH A1521  HOH A1558
SITE     3 AC1  9 HOH A1617
SITE     1 AC2  4 ARG A 224  LYS A 226  PHE A 227  HOH A1658
SITE     1 AC3 20 ARG A  36  ILE A  37  ARG A  54  ASP A  60
SITE     2 AC3 20 ASP A  97  GLU A 231  ARG A 246  ARG A 315
SITE     3 AC3 20 TYR A 343  PRO A 596  HOH A 908  HOH A 936
SITE     4 AC3 20 HOH A1153  HOH A1196  HOH A1261  HOH A1270
SITE     5 AC3 20 HOH A1319  HOH A1403  HOH A1422  HOH A1431
CRYST1   73.672   95.569  105.816  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      0.013574  0.000000  0.000000        0.00000
SCALE2      0.000000  0.010464  0.000000        0.00000
SCALE3      0.000000  0.000000  0.009450        0.00000
      
PROCHECK
Go to PROCHECK summary
 References