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PDBsum entry 3o9j

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Hydrolase PDB id
3o9j
Jmol
Contents
Protein chain
387 a.a.
Ligands
RP6
NDG
Metals
_CA
Waters ×320
HEADER    HYDROLASE                               04-AUG-10   3O9J
TITLE     INFLUENZA NA IN COMPLEX WITH COMPOUND 5
CAVEAT     3O9J    THERE ARE SEVERAL INCORRECT PEPTIDE BONDS IN CHAIN A
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: NEURAMINIDASE;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UNP RESIDUES 81-467;
COMPND   5 EC: 3.2.1.18
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS (A/DUCK/UKRAINE/1/1963(H3N8)
SOURCE   3 );
SOURCE   4 ORGANISM_TAXID: 385580;
SOURCE   5 STRAIN: A/DUCK/UKRAINE/1/1963 H3N8
KEYWDS    NEURAMINIDASE, HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    R.J.RUSSELL,P.S.KERRY
REVDAT   1   15-DEC-10 3O9J    0
JRNL        AUTH   S.RUDRAWAR,J.C.DYASON,M.A.RAMEIX-WELTI,F.J.ROSE,P.S.KERRY,
JRNL        AUTH 2 R.J.RUSSELL,S.VAN DER WERF,R.J.THOMSON,N.NAFFAKH,
JRNL        AUTH 3 M.VON ITZSTEIN
JRNL        TITL   NOVEL SIALIC ACID DERIVATIVES LOCK OPEN THE 150-LOOP OF AN
JRNL        TITL 2 INFLUENZA A VIRUS GROUP-1 SIALIDASE.
JRNL        REF    NAT COMMUN                    V.   1   113 2010
JRNL        REFN                   ESSN 2041-1723
JRNL        PMID   21081911
JRNL        DOI    10.1038/NCOMMS1114
REMARK   2
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.6_289)
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-
REMARK   3               : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,
REMARK   3               : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL
REMARK   3               : MORIARTY,REETAL PAI,RANDY READ,JANE
REMARK   3               : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM
REMARK   3               : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,
REMARK   3               : LAURENT STORONI,TOM TERWILLIGER,PETER
REMARK   3               : ZWART
REMARK   3
REMARK   3    REFINEMENT TARGET : ML
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 28.64
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.890
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.3
REMARK   3   NUMBER OF REFLECTIONS             : 27534
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.218
REMARK   3   R VALUE            (WORKING SET) : 0.215
REMARK   3   FREE R VALUE                     : 0.282
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.050
REMARK   3   FREE R VALUE TEST SET COUNT      : 1465
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE
REMARK   3     1 28.6468 -  4.3049    0.98     2833   127  0.2181 0.2323
REMARK   3     2  4.3049 -  3.4188    0.99     2812   169  0.1893 0.2405
REMARK   3     3  3.4188 -  2.9871    0.99     2806   143  0.1948 0.2883
REMARK   3     4  2.9871 -  2.7142    0.99     2822   130  0.1956 0.2867
REMARK   3     5  2.7142 -  2.5198    1.00     2811   153  0.1937 0.3024
REMARK   3     6  2.5198 -  2.3713    1.00     2806   165  0.2137 0.2608
REMARK   3     7  2.3713 -  2.2526    1.00     2806   161  0.2226 0.3487
REMARK   3     8  2.2526 -  2.1546    1.00     2774   160  0.2343 0.2953
REMARK   3     9  2.1546 -  2.0717    0.94     2666   135  0.2522 0.3648
REMARK   3    10  2.0717 -  2.0002    0.84     2393   122  0.2768 0.3721
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL
REMARK   3   SOLVENT RADIUS     : 1.11
REMARK   3   SHRINKAGE RADIUS   : 0.90
REMARK   3   K_SOL              : 0.40
REMARK   3   B_SOL              : 63.69
REMARK   3
REMARK   3  ERROR ESTIMATES.
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.330
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.890
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) : -9.34930
REMARK   3    B22 (A**2) : -9.34930
REMARK   3    B33 (A**2) : 18.69870
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  TWINNING INFORMATION.
REMARK   3   FRACTION: NULL
REMARK   3   OPERATOR: NULL
REMARK   3
REMARK   3  DEVIATIONS FROM IDEAL VALUES.
REMARK   3                 RMSD          COUNT
REMARK   3   BOND      :  0.018           3127
REMARK   3   ANGLE     :  1.825           4237
REMARK   3   CHIRALITY :  0.218            456
REMARK   3   PLANARITY :  0.010            546
REMARK   3   DIHEDRAL  : 21.293           1155
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  NCS DETAILS
REMARK   3   NUMBER OF NCS GROUPS : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3O9J COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-10.
REMARK 100 THE RCSB ID CODE IS RCSB060835.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 02-FEB-10
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 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          : RIGAKU
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 27534
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.000
REMARK 200  RESOLUTION RANGE LOW       (A) : 30.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.3
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) : 2.00
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.07
REMARK 200  COMPLETENESS FOR SHELL     (%) : 84.5
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: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 53.08
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD, PH 7, VAPOR DIFFUSION,
REMARK 280  HANGING DROP, TEMPERATURE 300K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4
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   -Y,X,Z
REMARK 290       4555   Y,-X,Z
REMARK 290       5555   X+1/2,Y+1/2,Z+1/2
REMARK 290       6555   -X+1/2,-Y+1/2,Z+1/2
REMARK 290       7555   -Y+1/2,X+1/2,Z+1/2
REMARK 290       8555   Y+1/2,-X+1/2,Z+1/2
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  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000       45.29000
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       45.29000
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       54.75000
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       45.29000
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       45.29000
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       54.75000
REMARK 290   SMTRY1   7  0.000000 -1.000000  0.000000       45.29000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000       45.29000
REMARK 290   SMTRY3   7  0.000000  0.000000  1.000000       54.75000
REMARK 290   SMTRY1   8  0.000000  1.000000  0.000000       45.29000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000       45.29000
REMARK 290   SMTRY3   8  0.000000  0.000000  1.000000       54.75000
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 14680 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 45150 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 KCAL/MOL
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   BIOMT1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   3  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT2   3  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   4  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT2   4 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   4  0.000000  0.000000  1.000000        0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375      HOH A 619  LIES ON A SPECIAL POSITION.
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    GLY A    96     O    GLY A   458              1.61
REMARK 500   O    MET A   346     N    GLY A   347              1.70
REMARK 500   O    PRO A   328     OE1  GLN A   350              1.74
REMARK 500   O    THR A   298     O    GLY A   347              2.01
REMARK 500   ND2  ASN A    86     O    HOH A   667              2.03
REMARK 500   N    THR A    83     O    HOH A    58              2.06
REMARK 500   CB   THR A   298     O    HOH A    40              2.12
REMARK 500   O    HOH A    68     O    HOH A   660              2.12
REMARK 500   NH2  ARG A   255     O    HOH A   710              2.13
REMARK 500   N    ASN A    87     O    HOH A   708              2.13
REMARK 500   OE1  GLU A   380     NZ   LYS A   399              2.18
REMARK 500   OE1  GLU A   443     CD1  LEU A   474              2.19
REMARK 500   NH1  ARG A   397     OE1  GLU A   462              2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   O    HOH A   572     O    HOH A   585     4545     2.15
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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   RES CSSEQI ATM2   DEVIATION
REMARK 500    TYR A 170   C     GLN A 172   N       0.220
REMARK 500    PRO A 310   N     PRO A 310   CA      0.132
REMARK 500    PRO A 310   CD    PRO A 310   N      -0.204
REMARK 500    GLN A 334   CB    GLN A 334   CG      0.286
REMARK 500    MET A 346   C     GLY A 347   N      -0.187
REMARK 500    GLN A 350   C     GLY A 351   N      -0.145
REMARK 500    LEU A 421   C     SER A 423   N       0.250
REMARK 500    LYS A 445   CB    LYS A 445   CG      0.694
REMARK 500    LYS A 445   C     THR A 446   N      -0.181
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    PRO A 310   N   -  CA  -  CB  ANGL. DEV. =  -8.5 DEGREES
REMARK 500    MET A 346   CA  -  C   -  N   ANGL. DEV. =  29.8 DEGREES
REMARK 500    MET A 346   O   -  C   -  N   ANGL. DEV. = -32.5 DEGREES
REMARK 500    GLY A 347   C   -  N   -  CA  ANGL. DEV. =  44.9 DEGREES
REMARK 500    GLN A 350   O   -  C   -  N   ANGL. DEV. = -12.0 DEGREES
REMARK 500    ASP A 364   CB  -  CG  -  OD1 ANGL. DEV. =   5.6 DEGREES
REMARK 500    ARG A 397   O   -  C   -  N   ANGL. DEV. = -13.1 DEGREES
REMARK 500    LEU A 421   O   -  C   -  N   ANGL. DEV. = -11.8 DEGREES
REMARK 500    LYS A 445   CA  -  CB  -  CG  ANGL. DEV. = -30.7 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    ARG A 111      -44.09   -136.79
REMARK 500    GLU A 119       74.35     44.06
REMARK 500    PRO A 126        2.24    -69.75
REMARK 500    ASN A 141       31.30     71.36
REMARK 500    THR A 148       14.13    -61.64
REMARK 500    ALA A 179      138.04   -171.77
REMARK 500    LYS A 202       60.08   -167.20
REMARK 500    THR A 227     -157.05   -140.78
REMARK 500    CYS A 232     -170.04    -67.65
REMARK 500    ASN A 249     -109.63   -117.24
REMARK 500    ARG A 250     -170.68    -24.74
REMARK 500    PHE A 272       55.31   -158.38
REMARK 500    TRP A 297      -68.56    -94.99
REMARK 500    LEU A 312       -2.97    111.42
REMARK 500    TYR A 352     -166.20     67.96
REMARK 500    THR A 391       30.52    -76.22
REMARK 500    SER A 409     -124.66   -127.42
REMARK 500    VAL A 459      135.88     70.42
REMARK 500    ASP A 460       34.92    -88.12
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 GLY A  147     THR A  148                  148.40
REMARK 500 PHE A  337     THR A  338                  148.69
REMARK 500 MET A  346     GLY A  347                  102.93
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    PHE A 337         10.02
REMARK 500    MET A 346         24.50
REMARK 500    ARG A 397         12.68
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 A 481        DISTANCE =  5.30 ANGSTROMS
REMARK 525    HOH A 486        DISTANCE =  6.80 ANGSTROMS
REMARK 525    HOH A 515        DISTANCE =  5.38 ANGSTROMS
REMARK 525    HOH A 519        DISTANCE =  5.03 ANGSTROMS
REMARK 525    HOH A 522        DISTANCE =  6.19 ANGSTROMS
REMARK 525    HOH A 523        DISTANCE =  5.17 ANGSTROMS
REMARK 525    HOH A 560        DISTANCE =  8.15 ANGSTROMS
REMARK 525    HOH A 564        DISTANCE =  6.28 ANGSTROMS
REMARK 525    HOH A 577        DISTANCE =  5.36 ANGSTROMS
REMARK 525    HOH A 580        DISTANCE =  7.44 ANGSTROMS
REMARK 525    HOH A 586        DISTANCE =  5.77 ANGSTROMS
REMARK 525    HOH A 597        DISTANCE =  5.20 ANGSTROMS
REMARK 525    HOH A 601        DISTANCE =  7.83 ANGSTROMS
REMARK 525    HOH A 620        DISTANCE =  5.20 ANGSTROMS
REMARK 525    HOH A 627        DISTANCE =  6.48 ANGSTROMS
REMARK 525    HOH A 632        DISTANCE =  6.12 ANGSTROMS
REMARK 525    HOH A 640        DISTANCE =  5.13 ANGSTROMS
REMARK 525    HOH A 649        DISTANCE =  5.28 ANGSTROMS
REMARK 525    HOH A 717        DISTANCE =  6.93 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 995  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 TYR A 352   O
REMARK 620 2 HOH A  67   O    79.6
REMARK 620 3 GLY A 299   O   170.7  92.3
REMARK 620 4 ASP A 295   O    87.3  79.2  86.6
REMARK 620 5 ASP A 326   OD1  99.6 159.4  86.2  80.2
REMARK 620 N                    1     2     3     4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RP6 A 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 995
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDG A 479
DBREF  3O9J A   83   478  UNP    Q07599   NRAM_I63A3      81    467
SEQADV 3O9J ASN A  296  UNP  Q07599    GLY   293 CONFLICT
SEQRES   1 A  387  THR TYR MET ASN ASN THR GLU ALA ILE CYS ASP ALA LYS
SEQRES   2 A  387  GLY PHE ALA PRO PHE SER LYS ASP ASN GLY ILE ARG ILE
SEQRES   3 A  387  GLY SER ARG GLY HIS ILE PHE VAL ILE ARG GLU PRO PHE
SEQRES   4 A  387  VAL SER CYS SER PRO ILE GLU CYS ARG THR PHE PHE LEU
SEQRES   5 A  387  THR GLN GLY SER LEU LEU ASN ASP LYS HIS SER ASN GLY
SEQRES   6 A  387  THR VAL LYS ASP ARG SER PRO PHE ARG THR LEU MET SER
SEQRES   7 A  387  VAL GLU VAL GLY GLN SER PRO ASN VAL TYR GLN ALA ARG
SEQRES   8 A  387  PHE GLU ALA VAL ALA TRP SER ALA THR ALA CYS HIS ASP
SEQRES   9 A  387  GLY LYS LYS TRP MET THR VAL GLY VAL THR GLY PRO ASP
SEQRES  10 A  387  SER LYS ALA VAL ALA VAL ILE HIS TYR GLY GLY VAL PRO
SEQRES  11 A  387  THR ASP VAL VAL ASN SER TRP ALA GLY ASP ILE LEU ARG
SEQRES  12 A  387  THR GLN GLU SER SER CYS THR CYS ILE GLN GLY ASP CYS
SEQRES  13 A  387  TYR TRP VAL MET THR ASP GLY PRO ALA ASN ARG GLN ALA
SEQRES  14 A  387  GLN TYR ARG ILE TYR LYS ALA ASN GLN GLY ARG ILE ILE
SEQRES  15 A  387  GLY GLN THR ASP ILE SER PHE ASN GLY GLY HIS ILE GLU
SEQRES  16 A  387  GLU CYS SER CYS TYR PRO ASN ASP GLY LYS VAL GLU CYS
SEQRES  17 A  387  VAL CYS ARG ASP ASN TRP THR GLY THR ASN ARG PRO VAL
SEQRES  18 A  387  LEU VAL ILE SER PRO ASP LEU SER TYR ARG VAL GLY TYR
SEQRES  19 A  387  LEU CYS ALA GLY ILE PRO SER ASP THR PRO ARG GLY GLU
SEQRES  20 A  387  ASP THR GLN PHE THR GLY SER CYS THR SER PRO MET GLY
SEQRES  21 A  387  ASN GLN GLY TYR GLY VAL LYS GLY PHE GLY PHE ARG GLN
SEQRES  22 A  387  GLY THR ASP VAL TRP MET GLY ARG THR ILE SER ARG THR
SEQRES  23 A  387  SER ARG SER GLY PHE GLU ILE LEU ARG ILE LYS ASN GLY
SEQRES  24 A  387  TRP THR GLN THR SER LYS GLU GLN ILE ARG LYS GLN VAL
SEQRES  25 A  387  VAL VAL ASP ASN LEU ASN TRP SER GLY TYR SER GLY SER
SEQRES  26 A  387  PHE THR LEU PRO VAL GLU LEU SER GLY LYS ASP CYS LEU
SEQRES  27 A  387  VAL PRO CYS PHE TRP VAL GLU MET ILE ARG GLY LYS PRO
SEQRES  28 A  387  GLU GLU LYS THR ILE TRP THR SER SER SER SER ILE VAL
SEQRES  29 A  387  MET CYS GLY VAL ASP TYR GLU VAL ALA ASP TRP SER TRP
SEQRES  30 A  387  HIS ASP GLY ALA ILE LEU PRO PHE ASP ILE
HET    RP6  A   1      23
HET     CA  A 995       1
HET    NDG  A 479      15
HETNAM     RP6 5-(ACETYLAMINO)-2,6-ANHYDRO-3,5-DIDEOXY-3-PROP-2-EN-1-
HETNAM   2 RP6  YL-D-GLYCERO-D-GALACTO-NON-2-ENONIC ACID
HETNAM      CA CALCIUM ION
HETNAM     NDG 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
FORMUL   2  RP6    C14 H21 N O8
FORMUL   3   CA    CA 2+
FORMUL   4  NDG    C8 H15 N O6
FORMUL   5  HOH   *320(H2 O)
HELIX    1   1 ASN A  104  GLY A  109  1                                   6
HELIX    2   2 ASP A  142  GLY A  147  5                                   6
HELIX    3   3 ASN A  168  ALA A  173  5                                   5
HELIX    4   4 PRO A  199  LYS A  202  5                                   4
HELIX    5   5 PRO A  418  GLY A  424  1                                   6
SHEET    1   A 4 ALA A  98  LYS A 102  0
SHEET    2   A 4 THR A 449  CYS A 457 -1  O  VAL A 455   N  PHE A 100
SHEET    3   A 4 VAL A 429  GLY A 439 -1  N  PHE A 432   O  MET A 456
SHEET    4   A 4 SER A 412  LEU A 417 -1  N  PHE A 415   O  CYS A 431
SHEET    1   B 4 PHE A 115  CYS A 124  0
SHEET    2   B 4 CYS A 129  LEU A 139 -1  O  PHE A 132   N  PHE A 121
SHEET    3   B 4 THR A 157  GLU A 162 -1  O  VAL A 161   N  THR A 131
SHEET    4   B 4 ARG A 174  VAL A 178 -1  O  ALA A 177   N  LEU A 158
SHEET    1   C 5 PRO A 213  ASN A 218  0
SHEET    2   C 5 VAL A 204  TYR A 209 -1  N  ILE A 207   O  THR A 214
SHEET    3   C 5 TRP A 191  THR A 197 -1  N  THR A 193   O  HIS A 208
SHEET    4   C 5 SER A 181  HIS A 186 -1  N  CYS A 185   O  MET A 192
SHEET    5   C 5 SER A 230  SER A 231  1  O  SER A 230   N  ALA A 184
SHEET    1   D 4 THR A 233  ILE A 235  0
SHEET    2   D 4 ASP A 238  ASP A 245 -1  O  TYR A 240   N  THR A 233
SHEET    3   D 4 GLN A 253  ASN A 260 -1  O  ALA A 259   N  CYS A 239
SHEET    4   D 4 ARG A 263  ASP A 269 -1  O  GLY A 266   N  LYS A 258
SHEET    1   E 4 GLU A 278  ASN A 285  0
SHEET    2   E 4 LYS A 288  ARG A 294 -1  O  LYS A 288   N  ASN A 285
SHEET    3   E 4 PRO A 303  ILE A 307 -1  O  ILE A 307   N  VAL A 289
SHEET    4   E 4 TYR A 314  TYR A 318 -1  O  ARG A 315   N  VAL A 306
SHEET    1   F 4 GLY A 358  GLN A 361  0
SHEET    2   F 4 ASP A 364  ARG A 369 -1  O  ASP A 364   N  GLN A 361
SHEET    3   F 4 SER A 377  ILE A 384 -1  O  LEU A 382   N  MET A 367
SHEET    4   F 4 GLN A 395  TRP A 408 -1  O  VAL A 403   N  PHE A 379
SSBOND   1 CYS A   92    CYS A  427                          1555   1555  2.05
SSBOND   2 CYS A  124    CYS A  129                          1555   1555  2.03
SSBOND   3 CYS A  185    CYS A  232                          1555   1555  2.03
SSBOND   4 CYS A  234    CYS A  239                          1555   1555  2.08
SSBOND   5 CYS A  280    CYS A  293                          1555   1555  2.03
SSBOND   6 CYS A  282    CYS A  291                          1555   1555  2.08
SSBOND   7 CYS A  320    CYS A  342                          1555   1555  2.02
SSBOND   8 CYS A  431    CYS A  457                          1555   1555  2.03
LINK         O   TYR A 352                CA    CA A 995     1555   1555  2.31
LINK        CA    CA A 995                 O   HOH A  67     1555   1555  2.42
LINK         O   GLY A 299                CA    CA A 995     1555   1555  2.47
LINK         O   ASP A 295                CA    CA A 995     1555   1555  2.50
LINK         OD1 ASP A 326                CA    CA A 995     1555   1555  2.57
CISPEP   1 THR A  327    PRO A  328          0         4.99
CISPEP   2 LYS A  440    PRO A  441          0        -5.99
CISPEP   3 LEU A  474    PRO A  475          0        -7.62
SITE     1 AC1 15 HOH A  38  HOH A  49  HOH A  70  HOH A  73
SITE     2 AC1 15 ARG A 118  ARG A 152  TRP A 180  ALA A 248
SITE     3 AC1 15 GLU A 278  GLU A 279  ARG A 294  ASN A 296
SITE     4 AC1 15 ARG A 376  TYR A 411  HOH A 656
SITE     1 AC2  5 HOH A  67  ASP A 295  GLY A 299  ASP A 326
SITE     2 AC2  5 TYR A 352
SITE     1 AC3  2 ASN A 146  THR A 148
CRYST1   90.580   90.580  109.500  90.00  90.00  90.00 I 4           8
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      0.011040  0.000000  0.000000        0.00000
SCALE2      0.000000  0.011040  0.000000        0.00000
SCALE3      0.000000  0.000000  0.009132        0.00000
      
PROCHECK
Go to PROCHECK summary
 References