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PDBsum entry 2xzi

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Hydrolase PDB id
2xzi
Jmol
Contents
Protein chains
385 a.a.
Ligands
KDM ×4
GOL ×5
NO2
Metals
_NA ×2
Waters ×1155
HEADER    HYDROLASE                               26-NOV-10   2XZI
TITLE     THE ASPERGILLUS FUMIGATUS SIALIDASE IS A KDNASE:
TITLE    2 STRUCTURAL AND MECHANISTIC INSIGHTS
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE;
COMPND   3 CHAIN: A, B;
COMPND   4 FRAGMENT: RESIDUES 21-406;
COMPND   5 SYNONYM: KDNASE;
COMPND   6 EC: 3.2.1.18;
COMPND   7 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: ASPERGILLUS FUMIGATUS;
SOURCE   3 ORGANISM_TAXID: 330879;
SOURCE   4 STRAIN: AF293;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21
KEYWDS    HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    J.C.TELFORD,J.H.F.YEUNG,M.J.KIEFEL,A.G.WATTS,S.HADER,J.CHAN,
AUTHOR   2 A.J.BENNET,M.M.MOORE,G.L.TAYLOR
REVDAT   3   17-AUG-11 2XZI    1       JRNL   REMARK HETSYN VERSN
REVDAT   2   02-FEB-11 2XZI    1       JRNL
REVDAT   1   19-JAN-11 2XZI    0
JRNL        AUTH   J.C.TELFORD,J.H.F.YEUNG,G.XU,M.J.KIEFEL,A.G.WATTS,
JRNL        AUTH 2 S.HADER,J.CHAN,A.J.BENNET,M.M.MOORE,G.L.TAYLOR
JRNL        TITL   THE ASPERGILLUS FUMIGATUS SIALIDASE IS A KDNASE:
JRNL        TITL 2 STRUCTURAL AND MECHANISTIC INSIGHTS.
JRNL        REF    J.BIOL.CHEM.                  V. 286 10783 2011
JRNL        REFN                   ISSN 0021-9258
JRNL        PMID   21247893
JRNL        DOI    10.1074/JBC.M110.207043
REMARK   2
REMARK   2 RESOLUTION.    1.45 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.5.0109
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) : 1.45
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 37.31
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NONE
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.33
REMARK   3   NUMBER OF REFLECTIONS             : 135232
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) : 0.18045
REMARK   3   R VALUE            (WORKING SET) : 0.17917
REMARK   3   FREE R VALUE                     : 0.20459
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.0
REMARK   3   FREE R VALUE TEST SET COUNT      : 7087
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) : 1.451
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.489
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 9541
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 95.10
REMARK   3   BIN R VALUE           (WORKING SET) : 0.255
REMARK   3   BIN FREE R VALUE SET COUNT          : 479
REMARK   3   BIN FREE R VALUE                    : 0.277
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 6021
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 107
REMARK   3   SOLVENT ATOMS            : 1155
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 12.220
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.03
REMARK   3    B22 (A**2) : 0.27
REMARK   3    B33 (A**2) : -0.28
REMARK   3    B12 (A**2) : 0.00
REMARK   3    B13 (A**2) : -0.09
REMARK   3    B23 (A**2) : 0.00
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): 0.069
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.070
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.044
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.093
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.948
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.934
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  6287 ; 0.009 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  8567 ; 1.286 ; 1.958
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   809 ; 6.551 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   298 ;30.431 ;23.087
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   969 ;12.088 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    61 ;15.328 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   906 ; 0.078 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  4925 ; 0.007 ; 0.021
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):  NULL ;  NULL ;  NULL
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):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):  NULL ;  NULL ;  NULL
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):  3861 ; 0.615 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  6199 ; 1.046 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  2426 ; 1.624 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  2347 ; 2.495 ; 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 : MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
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 2XZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-10.
REMARK 100 THE PDBE ID CODE IS EBI-46409.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : NULL
REMARK 200  NUMBER OF CRYSTALS USED        : NULL
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : ID29
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9794
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALA
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 143277
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.45
REMARK 200  RESOLUTION RANGE LOW       (A) : 37.30
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.5
REMARK 200  DATA REDUNDANCY                : 3.5
REMARK 200  R MERGE                    (I) : 0.08
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 9.40
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.53
REMARK 200  COMPLETENESS FOR SHELL     (%) : 97.6
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.4
REMARK 200  R MERGE FOR SHELL          (I) : 0.24
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 4.30
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NONE
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 38.40
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,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       28.99500
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
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     ILE A    21
REMARK 465     ILE B    21
REMARK 465     ASN B    22
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     ASN A 406    CB   CG   OD1  ND2
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 B  2158     O    HOH B  2364              2.08
REMARK 500   O    ASN A   379     O    HOH A  2543              2.11
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    ILE A  60       64.56     65.95
REMARK 500    ALA A 201      -85.18   -112.05
REMARK 500    ASN A 235       47.32   -141.27
REMARK 500    ALA A 295       69.96     65.36
REMARK 500    THR A 320      -31.17   -130.27
REMARK 500    ILE B  60       62.84     68.49
REMARK 500    ASN B 101       18.78     59.17
REMARK 500    ALA B 201      -84.95   -110.91
REMARK 500    ALA B 295       70.08     64.55
REMARK 500    THR B 320      -34.40   -130.91
REMARK 500    ARG B 323       34.74    -99.63
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KDM A 500
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KDM A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  NA A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO2 A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KDM B 500
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KDM B 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  NA B 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 505
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2XZJ   RELATED DB: PDB
REMARK 900  THE ASPERGILLUS FUMIGATUS SIALIDASE IS A
REMARK 900  KDNASE: STRUCTURAL AND MECHANISTIC INSIGHTS
REMARK 900 RELATED ID: 2XCY   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF ASPERGILLUS FUMIGATUS
REMARK 900  SIALIDASE
REMARK 900 RELATED ID: 2XZK   RELATED DB: PDB
REMARK 900  THE ASPERGILLUS FUMIGATUS SIALIDASE IS A
REMARK 900  KDNASE: STRUCTURAL AND MECHANISTIC INSIGHTS
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 CRYSTALLIZED PROTEIN LACKS FIRST 20 AMINO ACIDS (SIGNAL
REMARK 999 SEQUENCE)
DBREF  2XZI A   21   406  UNP    Q4WQS0   Q4WQS0_ASPFU    21    406
DBREF  2XZI B   21   406  UNP    Q4WQS0   Q4WQS0_ASPFU    21    406
SEQRES   1 A  386  ILE ASN ASP PRO ALA LYS SER ALA ALA PRO TYR HIS ASP
SEQRES   2 A  386  GLU PHE PRO LEU PHE ARG SER ALA ASN MET ALA SER PRO
SEQRES   3 A  386  ASP LYS LEU SER THR GLY ILE GLY PHE HIS SER PHE ARG
SEQRES   4 A  386  ILE PRO ALA VAL VAL ARG THR THR THR GLY ARG ILE LEU
SEQRES   5 A  386  ALA PHE ALA GLU GLY ARG ARG HIS THR ASN GLN ASP PHE
SEQRES   6 A  386  GLY ASP ILE ASN LEU VAL TYR LYS ARG THR LYS THR THR
SEQRES   7 A  386  ALA ASN ASN GLY ALA SER PRO SER ASP TRP GLU PRO LEU
SEQRES   8 A  386  ARG GLU VAL VAL GLY SER GLY ALA GLY THR TRP GLY ASN
SEQRES   9 A  386  PRO THR PRO VAL VAL ASP ASP ASP ASN THR ILE TYR LEU
SEQRES  10 A  386  PHE LEU SER TRP ASN GLY ALA THR TYR SER GLN ASN GLY
SEQRES  11 A  386  LYS ASP VAL LEU PRO ASP GLY THR VAL THR LYS LYS ILE
SEQRES  12 A  386  ASP SER THR TRP GLU GLY ARG ARG HIS LEU TYR LEU THR
SEQRES  13 A  386  GLU SER ARG ASP ASP GLY ASN THR TRP SER LYS PRO VAL
SEQRES  14 A  386  ASP LEU THR LYS GLU LEU THR PRO ASP GLY TRP ALA TRP
SEQRES  15 A  386  ASP ALA VAL GLY PRO GLY ASN GLY ILE ARG LEU THR THR
SEQRES  16 A  386  GLY GLU LEU VAL ILE PRO ALA MET GLY ARG ASN ILE ILE
SEQRES  17 A  386  GLY ARG GLY ALA PRO GLY ASN ARG THR TRP SER VAL GLN
SEQRES  18 A  386  ARG LEU SER GLY ALA GLY ALA GLU GLY THR ILE VAL GLN
SEQRES  19 A  386  THR PRO ASP GLY LYS LEU TYR ARG ASN ASP ARG PRO SER
SEQRES  20 A  386  GLN LYS GLY TYR ARG MET VAL ALA ARG GLY THR LEU GLU
SEQRES  21 A  386  GLY PHE GLY ALA PHE ALA PRO ASP ALA GLY LEU PRO ASP
SEQRES  22 A  386  PRO ALA CYS GLN GLY SER VAL LEU ARG TYR ASN SER ASP
SEQRES  23 A  386  ALA PRO ALA ARG THR ILE PHE LEU ASN SER ALA SER GLY
SEQRES  24 A  386  THR SER ARG ARG ALA MET ARG VAL ARG ILE SER TYR ASP
SEQRES  25 A  386  ALA ASP ALA LYS LYS PHE ASN TYR GLY ARG LYS LEU GLU
SEQRES  26 A  386  ASP ALA LYS VAL SER GLY ALA GLY HIS GLU GLY GLY TYR
SEQRES  27 A  386  SER SER MET THR LYS THR GLY ASP TYR LYS ILE GLY ALA
SEQRES  28 A  386  LEU VAL GLU SER ASP PHE PHE ASN ASP GLY THR GLY LYS
SEQRES  29 A  386  ASN SER TYR ARG ALA ILE ILE TRP ARG ARG PHE ASN LEU
SEQRES  30 A  386  SER TRP ILE LEU ASN GLY PRO ASN ASN
SEQRES   1 B  386  ILE ASN ASP PRO ALA LYS SER ALA ALA PRO TYR HIS ASP
SEQRES   2 B  386  GLU PHE PRO LEU PHE ARG SER ALA ASN MET ALA SER PRO
SEQRES   3 B  386  ASP LYS LEU SER THR GLY ILE GLY PHE HIS SER PHE ARG
SEQRES   4 B  386  ILE PRO ALA VAL VAL ARG THR THR THR GLY ARG ILE LEU
SEQRES   5 B  386  ALA PHE ALA GLU GLY ARG ARG HIS THR ASN GLN ASP PHE
SEQRES   6 B  386  GLY ASP ILE ASN LEU VAL TYR LYS ARG THR LYS THR THR
SEQRES   7 B  386  ALA ASN ASN GLY ALA SER PRO SER ASP TRP GLU PRO LEU
SEQRES   8 B  386  ARG GLU VAL VAL GLY SER GLY ALA GLY THR TRP GLY ASN
SEQRES   9 B  386  PRO THR PRO VAL VAL ASP ASP ASP ASN THR ILE TYR LEU
SEQRES  10 B  386  PHE LEU SER TRP ASN GLY ALA THR TYR SER GLN ASN GLY
SEQRES  11 B  386  LYS ASP VAL LEU PRO ASP GLY THR VAL THR LYS LYS ILE
SEQRES  12 B  386  ASP SER THR TRP GLU GLY ARG ARG HIS LEU TYR LEU THR
SEQRES  13 B  386  GLU SER ARG ASP ASP GLY ASN THR TRP SER LYS PRO VAL
SEQRES  14 B  386  ASP LEU THR LYS GLU LEU THR PRO ASP GLY TRP ALA TRP
SEQRES  15 B  386  ASP ALA VAL GLY PRO GLY ASN GLY ILE ARG LEU THR THR
SEQRES  16 B  386  GLY GLU LEU VAL ILE PRO ALA MET GLY ARG ASN ILE ILE
SEQRES  17 B  386  GLY ARG GLY ALA PRO GLY ASN ARG THR TRP SER VAL GLN
SEQRES  18 B  386  ARG LEU SER GLY ALA GLY ALA GLU GLY THR ILE VAL GLN
SEQRES  19 B  386  THR PRO ASP GLY LYS LEU TYR ARG ASN ASP ARG PRO SER
SEQRES  20 B  386  GLN LYS GLY TYR ARG MET VAL ALA ARG GLY THR LEU GLU
SEQRES  21 B  386  GLY PHE GLY ALA PHE ALA PRO ASP ALA GLY LEU PRO ASP
SEQRES  22 B  386  PRO ALA CYS GLN GLY SER VAL LEU ARG TYR ASN SER ASP
SEQRES  23 B  386  ALA PRO ALA ARG THR ILE PHE LEU ASN SER ALA SER GLY
SEQRES  24 B  386  THR SER ARG ARG ALA MET ARG VAL ARG ILE SER TYR ASP
SEQRES  25 B  386  ALA ASP ALA LYS LYS PHE ASN TYR GLY ARG LYS LEU GLU
SEQRES  26 B  386  ASP ALA LYS VAL SER GLY ALA GLY HIS GLU GLY GLY TYR
SEQRES  27 B  386  SER SER MET THR LYS THR GLY ASP TYR LYS ILE GLY ALA
SEQRES  28 B  386  LEU VAL GLU SER ASP PHE PHE ASN ASP GLY THR GLY LYS
SEQRES  29 B  386  ASN SER TYR ARG ALA ILE ILE TRP ARG ARG PHE ASN LEU
SEQRES  30 B  386  SER TRP ILE LEU ASN GLY PRO ASN ASN
HET    KDM  A 500      18
HET    KDM  A 501      18
HET     NA  A 502       1
HET    GOL  A 503       6
HET    GOL  A 504       6
HET    NO2  A 505       3
HET    KDM  B 500      18
HET    KDM  B 501      18
HET     NA  B 502       1
HET    GOL  B 503       6
HET    GOL  B 504       6
HET    GOL  B 505       6
HETNAM     KDM (2R,4S,5R,6R)-2,4,5-TRIHYDROXY-6-[(1R,2R)-1,
HETNAM   2 KDM  2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC-ACID
HETNAM      NA SODIUM ION
HETNAM     GOL GLYCEROL
HETNAM     NO2 NITRITE ION
HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL   3  KDM    4(C9 H16 O9)
FORMUL   4   NA    2(NA 1+)
FORMUL   5  GOL    5(C3 H8 O3)
FORMUL   6  NO2    N O2 1-
FORMUL   7  HOH   *1155(H2 O)
HELIX    1   1 ASP A   23  ALA A   28  5                                   6
HELIX    2   2 SER A  104  ASP A  107  5                                   4
HELIX    3   3 LEU A  191  THR A  196  1                                   6
HELIX    4   4 GLU A  345  LYS A  348  5                                   4
HELIX    5   5 ASN A  396  ASN A  402  1                                   7
HELIX    6   6 ASP B   23  ALA B   28  5                                   6
HELIX    7   7 SER B  104  ASP B  107  5                                   4
HELIX    8   8 LEU B  191  THR B  196  1                                   6
HELIX    9   9 GLU B  345  LYS B  348  5                                   4
HELIX   10  10 ASN B  396  ASN B  402  1                                   7
SHEET    1  AA 4 HIS A  32  PHE A  38  0
SHEET    2  AA 4 ARG A 388  PHE A 395 -1  O  ILE A 390   N  LEU A  37
SHEET    3  AA 4 ILE A 369  ASP A 376 -1  O  ILE A 369   N  PHE A 395
SHEET    4  AA 4 HIS A 354  LYS A 363 -1  O  HIS A 354   N  ASP A 376
SHEET    1  AB 4 SER A  57  ARG A  65  0
SHEET    2  AB 4 ILE A  71  ARG A  78 -1  O  LEU A  72   N  VAL A  64
SHEET    3  AB 4 ILE A  88  ARG A  94 -1  O  ASN A  89   N  GLY A  77
SHEET    4  AB 4 ARG A 112  VAL A 115 -1  O  ARG A 112   N  TYR A  92
SHEET    1  AC 4 THR A 121  VAL A 129  0
SHEET    2  AC 4 ILE A 135  ASN A 142 -1  O  TYR A 136   N  VAL A 128
SHEET    3  AC 4 HIS A 172  SER A 178 -1  O  HIS A 172   N  TRP A 141
SHEET    4  AC 4 VAL A 189  ASP A 190 -1  O  VAL A 189   N  LEU A 175
SHEET    1  AD 2 TYR A 146  SER A 147  0
SHEET    2  AD 2 LYS A 161  LYS A 162  1  O  LYS A 161   N  SER A 147
SHEET    1  AE 4 ILE A 211  ARG A 212  0
SHEET    2  AE 4 LEU A 218  ALA A 222 -1  O  VAL A 219   N  ILE A 211
SHEET    3  AE 4 ARG A 225  ARG A 230 -1  O  ARG A 225   N  ALA A 222
SHEET    4  AE 4 THR A 237  ARG A 242 -1  O  THR A 237   N  ARG A 230
SHEET    1  AF 4 GLY A 250  GLN A 254  0
SHEET    2  AF 4 LEU A 260  ASP A 264 -1  O  TYR A 261   N  VAL A 253
SHEET    3  AF 4 GLY A 270  THR A 278 -1  O  MET A 273   N  ASP A 264
SHEET    4  AF 4 GLY A 281  PHE A 282  1  O  GLY A 281   N  THR A 278
SHEET    1  AG 4 GLY A 250  GLN A 254  0
SHEET    2  AG 4 LEU A 260  ASP A 264 -1  O  TYR A 261   N  VAL A 253
SHEET    3  AG 4 GLY A 270  THR A 278 -1  O  MET A 273   N  ASP A 264
SHEET    4  AG 4 ALA A 286  ASP A 293 -1  O  ALA A 286   N  VAL A 274
SHEET    1  AH 2 GLY A 281  PHE A 282  0
SHEET    2  AH 2 GLY A 270  THR A 278  1  O  THR A 278   N  GLY A 281
SHEET    1  AI 4 SER A 299  ASN A 304  0
SHEET    2  AI 4 ARG A 310  SER A 316 -1  O  ARG A 310   N  TYR A 303
SHEET    3  AI 4 MET A 325  SER A 330 -1  O  ARG A 326   N  ASN A 315
SHEET    4  AI 4 ARG A 342  LYS A 343 -1  O  ARG A 342   N  VAL A 327
SHEET    1  BA 4 HIS B  32  PHE B  38  0
SHEET    2  BA 4 ARG B 388  PHE B 395 -1  O  ILE B 390   N  LEU B  37
SHEET    3  BA 4 ILE B 369  ASP B 376 -1  O  ILE B 369   N  PHE B 395
SHEET    4  BA 4 HIS B 354  LYS B 363 -1  O  HIS B 354   N  ASP B 376
SHEET    1  BB 4 SER B  57  ARG B  65  0
SHEET    2  BB 4 ILE B  71  ARG B  78 -1  O  LEU B  72   N  VAL B  64
SHEET    3  BB 4 ILE B  88  ARG B  94 -1  O  ASN B  89   N  GLY B  77
SHEET    4  BB 4 ARG B 112  VAL B 115 -1  O  ARG B 112   N  TYR B  92
SHEET    1  BC 4 THR B 121  VAL B 129  0
SHEET    2  BC 4 ILE B 135  ASN B 142 -1  O  TYR B 136   N  VAL B 128
SHEET    3  BC 4 HIS B 172  SER B 178 -1  O  HIS B 172   N  TRP B 141
SHEET    4  BC 4 VAL B 189  ASP B 190 -1  O  VAL B 189   N  LEU B 175
SHEET    1  BD 2 TYR B 146  SER B 147  0
SHEET    2  BD 2 LYS B 161  LYS B 162  1  O  LYS B 161   N  SER B 147
SHEET    1  BE 4 ILE B 211  ARG B 212  0
SHEET    2  BE 4 LEU B 218  ALA B 222 -1  O  VAL B 219   N  ILE B 211
SHEET    3  BE 4 ARG B 225  ARG B 230 -1  O  ARG B 225   N  ALA B 222
SHEET    4  BE 4 THR B 237  ARG B 242 -1  O  THR B 237   N  ARG B 230
SHEET    1  BF 4 GLY B 250  GLN B 254  0
SHEET    2  BF 4 LEU B 260  ASP B 264 -1  O  TYR B 261   N  VAL B 253
SHEET    3  BF 4 GLY B 270  THR B 278 -1  O  MET B 273   N  ASP B 264
SHEET    4  BF 4 GLY B 281  PHE B 282  1  O  GLY B 281   N  THR B 278
SHEET    1  BG 4 GLY B 250  GLN B 254  0
SHEET    2  BG 4 LEU B 260  ASP B 264 -1  O  TYR B 261   N  VAL B 253
SHEET    3  BG 4 GLY B 270  THR B 278 -1  O  MET B 273   N  ASP B 264
SHEET    4  BG 4 ALA B 286  ASP B 293 -1  O  ALA B 286   N  VAL B 274
SHEET    1  BH 2 GLY B 281  PHE B 282  0
SHEET    2  BH 2 GLY B 270  THR B 278  1  O  THR B 278   N  GLY B 281
SHEET    1  BI 4 SER B 299  ASN B 304  0
SHEET    2  BI 4 ARG B 310  SER B 316 -1  O  ARG B 310   N  TYR B 303
SHEET    3  BI 4 MET B 325  SER B 330 -1  O  ARG B 326   N  ASN B 315
SHEET    4  BI 4 ARG B 342  LYS B 343 -1  O  ARG B 342   N  VAL B 327
CISPEP   1 GLY A  206    PRO A  207          0         4.76
CISPEP   2 ALA A  307    PRO A  308          0        -6.91
CISPEP   3 GLY B  206    PRO B  207          0         8.80
CISPEP   4 ALA B  307    PRO B  308          0        -9.37
SITE     1 AC1 17 ARG A  59  ARG A  78  ASP A  84  GLN A 148
SITE     2 AC1 17 TRP A 202  GLU A 249  ARG A 265  ARG A 322
SITE     3 AC1 17 TYR A 358  HOH A2130  HOH A2396  HOH A2572
SITE     4 AC1 17 HOH A2573  HOH A2574  HOH A2576  HOH A2577
SITE     5 AC1 17 HOH A2581
SITE     1 AC2 13 SER A 321  ARG A 322  ARG A 323  ASP A 376
SITE     2 AC2 13 ARG A 388  HOH A2526  HOH A2539  HOH A2579
SITE     3 AC2 13 HOH A2580  HOH A2581  HOH A2582  HOH A2583
SITE     4 AC2 13 HOH A2584
SITE     1 AC3  6 ASP A  87  ASN A  89  GLY A 116  GLY A 118
SITE     2 AC3  6 HOH A2168  HOH A2237
SITE     1 AC4  8 LEU A 213  THR A 215  GLY A 258  LYS A 259
SITE     2 AC4  8 THR A 278  LEU A 279  HOH A2585  HOH A2586
SITE     1 AC5  8 ASP A 132  ASN A 133  THR A 134  ARG A 179
SITE     2 AC5  8 HOH A2253  HOH A2587  HOH A2588  HOH A2589
SITE     1 AC6  4 ARG A 230  SER A 239  LEU A 279  HOH A2591
SITE     1 AC7 15 ARG B  59  ARG B  78  ASP B  84  GLN B 148
SITE     2 AC7 15 TRP B 202  GLU B 249  ARG B 265  ARG B 322
SITE     3 AC7 15 TYR B 358  GOL B 505  HOH B2373  HOH B2550
SITE     4 AC7 15 HOH B2551  HOH B2552  HOH B2553
SITE     1 AC8 11 SER B 321  ARG B 322  ARG B 323  ASP B 376
SITE     2 AC8 11 ARG B 388  HOH B2523  HOH B2535  HOH B2555
SITE     3 AC8 11 HOH B2556  HOH B2557  HOH B2558
SITE     1 AC9  6 ASP B  87  ASN B  89  GLY B 116  GLY B 118
SITE     2 AC9  6 HOH B2148  HOH B2211
SITE     1 BC1  8 THR B 215  GLY B 258  LYS B 259  THR B 278
SITE     2 BC1  8 LEU B 279  HOH B2559  HOH B2560  HOH B2561
SITE     1 BC2  7 ASP B 132  ASN B 133  THR B 134  ARG B 179
SITE     2 BC2  7 HOH B2562  HOH B2563  HOH B2564
SITE     1 BC3  7 ARG B  59  ARG B  78  ASN B  82  ASP B  84
SITE     2 BC3  7 ARG B 388  KDM B 500  HOH B2137
CRYST1   75.810   57.990   94.830  90.00 100.14  90.00 P 1 21 1      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      0.013191  0.000000  0.002359        0.00000
SCALE2      0.000000  0.017244  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010713        0.00000
      
PROCHECK
Go to PROCHECK summary
 References