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PDBsum entry 4g3y

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Top Page protein Protein-protein interface(s) links
Immune system PDB id
4g3y
Jmol
Contents
Protein chains
214 a.a.
220 a.a.
148 a.a.
Waters ×134
HEADER    IMMUNE SYSTEM                           15-JUL-12   4G3Y
TITLE     CRYSTAL STRUCTURE OF TNF-ALPHA IN COMPLEX WITH INFLIXIMAB FAB FRAGMENT
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: INFLIXIMAB FAB L;
COMPND   3 CHAIN: L;
COMPND   4 ENGINEERED: YES;
COMPND   5 MOL_ID: 2;
COMPND   6 MOLECULE: INFLIXIMAB FAB H;
COMPND   7 CHAIN: H;
COMPND   8 ENGINEERED: YES;
COMPND   9 MOL_ID: 3;
COMPND  10 MOLECULE: TUMOR NECROSIS FACTOR;
COMPND  11 CHAIN: C;
COMPND  12 FRAGMENT: TUMOR NECROSIS FACTOR, SOLUBLE FORM;
COMPND  13 SYNONYM: TNF-ALPHA;
COMPND  14 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   7 MOL_ID: 2;
SOURCE   8 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   9 ORGANISM_COMMON: HUMAN;
SOURCE  10 ORGANISM_TAXID: 9606;
SOURCE  11 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE  12 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE  13 MOL_ID: 3;
SOURCE  14 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE  15 ORGANISM_COMMON: HUMAN;
SOURCE  16 ORGANISM_TAXID: 9606;
SOURCE  17 GENE: TNFA;
SOURCE  18 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE  19 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    TNF, INFLIXIMAB, IMMUNE SYSTEM
EXPDTA    X-RAY DIFFRACTION
AUTHOR    S.Y.LIANG,J.X.DAI,Y.J.GUO,Z.Y.LOU
REVDAT   2   07-AUG-13 4G3Y    1       JRNL
REVDAT   1   27-MAR-13 4G3Y    0
JRNL        AUTH   S.Y.LIANG,J.X.DAI,S.HOU,L.SU,D.ZHANG,H.GUO,S.HU,H.WANG,
JRNL        AUTH 2 Z.RAO,Y.J.GUO,Z.Y.LOU
JRNL        TITL   STRUCTURAL BASIS FOR TREATING TUMOR NECROSIS FACTOR ALPHA
JRNL        TITL 2 (TNFALPHA)-ASSOCIATED DISEASES WITH THE THERAPEUTIC ANTIBODY
JRNL        TITL 3 INFLIXIMAB
JRNL        REF    J.BIOL.CHEM.                  V. 288 13799 2013
JRNL        REFN                   ISSN 0021-9258
JRNL        PMID   23504311
JRNL        DOI    10.1074/JBC.M112.433961
REMARK   2
REMARK   2 RESOLUTION.    2.60 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.6.1_357)
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) : 2.60
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 21.54
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 0.080
REMARK   3   COMPLETENESS FOR RANGE        (%) : 94.5
REMARK   3   NUMBER OF REFLECTIONS             : 25400
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.191
REMARK   3   R VALUE            (WORKING SET) : 0.189
REMARK   3   FREE R VALUE                     : 0.235
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.030
REMARK   3   FREE R VALUE TEST SET COUNT      : 1278
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 21.5356 -  5.3832    0.99     2828   143  0.1711 0.2087
REMARK   3     2  5.3832 -  4.2838    0.99     2808   141  0.1316 0.1656
REMARK   3     3  4.2838 -  3.7456    0.98     2779   161  0.1556 0.1925
REMARK   3     4  3.7456 -  3.4046    0.98     2787   135  0.1871 0.2389
REMARK   3     5  3.4046 -  3.1613    0.97     2719   147  0.2152 0.2614
REMARK   3     6  3.1613 -  2.9755    0.95     2725   161  0.2308 0.3108
REMARK   3     7  2.9755 -  2.8268    0.93     2627   146  0.2480 0.2942
REMARK   3     8  2.8268 -  2.7040    0.88     2483   122  0.2452 0.3081
REMARK   3     9  2.7040 -  2.6001    0.82     2366   122  0.2485 0.3149
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              : 0.34
REMARK   3   B_SOL              : 31.58
REMARK   3
REMARK   3  ERROR ESTIMATES.
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.330
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.550
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 38.91
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -1.62390
REMARK   3    B22 (A**2) : -1.62390
REMARK   3    B33 (A**2) : 3.24780
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      :  0.008           4576
REMARK   3   ANGLE     :  1.223           6214
REMARK   3   CHIRALITY :  0.079            695
REMARK   3   PLANARITY :  0.005            800
REMARK   3   DIHEDRAL  : 16.588           1647
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 4G3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-12.
REMARK 100 THE RCSB ID CODE IS RCSB073707.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 05-SEP-10
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 8.2
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : PHOTON FACTORY
REMARK 200  BEAMLINE                       : BL-17A
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.0000
REMARK 200  MONOCHROMATOR                  : SAGITALLY FOCUSED SI(111)
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315R
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 27025
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.600
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.0
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 64.45
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M NA/K PHOSPHATE, PH 8.2, VAPOR
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -Y,X-Y,Z
REMARK 290       3555   -X+Y,-X,Z
REMARK 290       4555   X+2/3,Y+1/3,Z+1/3
REMARK 290       5555   -Y+2/3,X-Y+1/3,Z+1/3
REMARK 290       6555   -X+Y+2/3,-X+1/3,Z+1/3
REMARK 290       7555   X+1/3,Y+2/3,Z+2/3
REMARK 290       8555   -Y+1/3,X-Y+2/3,Z+2/3
REMARK 290       9555   -X+Y+1/3,-X+2/3,Z+2/3
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 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       76.83150
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       44.35869
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       33.09300
REMARK 290   SMTRY1   5 -0.500000 -0.866025  0.000000       76.83150
REMARK 290   SMTRY2   5  0.866025 -0.500000  0.000000       44.35869
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       33.09300
REMARK 290   SMTRY1   6 -0.500000  0.866025  0.000000       76.83150
REMARK 290   SMTRY2   6 -0.866025 -0.500000  0.000000       44.35869
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       33.09300
REMARK 290   SMTRY1   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       88.71737
REMARK 290   SMTRY3   7  0.000000  0.000000  1.000000       66.18600
REMARK 290   SMTRY1   8 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   8  0.866025 -0.500000  0.000000       88.71737
REMARK 290   SMTRY3   8  0.000000  0.000000  1.000000       66.18600
REMARK 290   SMTRY1   9 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   9 -0.866025 -0.500000  0.000000       88.71737
REMARK 290   SMTRY3   9  0.000000  0.000000  1.000000       66.18600
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: NONAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, C
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 -0.500000 -0.866025  0.000000        0.00000
REMARK 350   BIOMT2   2  0.866025 -0.500000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   3 -0.500000  0.866025  0.000000        0.00000
REMARK 350   BIOMT2   3 -0.866025 -0.500000  0.000000        0.00000
REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5200 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25300 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, C
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     LYS H   221
REMARK 465     SER H   222
REMARK 465     CYS H   223
REMARK 465     ASP H   224
REMARK 465     LYS H   225
REMARK 465     THR H   226
REMARK 465     VAL C     1
REMARK 465     ARG C     2
REMARK 465     SER C     3
REMARK 465     SER C     4
REMARK 465     SER C     5
REMARK 465     ARG C     6
REMARK 465     THR C     7
REMARK 465     PRO C     8
REMARK 465     SER C     9
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     TYR C  87    CG   CD1  CD2  CE1  CE2  CZ   OH
REMARK 470     LEU C 157    O
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 C 106   C   -  N   -  CA  ANGL. DEV. =  11.5 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 L  51      -44.79     71.17
REMARK 500    SER L  52       -7.42   -143.76
REMARK 500    THR L  69      -14.32   -142.08
REMARK 500    SER L 127        3.34    -55.81
REMARK 500    ASP L 151       53.65     39.22
REMARK 500    SER L 171       19.35     59.85
REMARK 500    GLU L 187        1.23    -64.79
REMARK 500    VAL H   2       96.69     57.30
REMARK 500    ASN H  57      176.73     57.25
REMARK 500    ALA H  59       88.96     50.27
REMARK 500    SER H 105      -92.54   -156.37
REMARK 500    SER H 137       58.25    -91.52
REMARK 500    SER H 139       71.16     13.38
REMARK 500    ASP H 151       79.45     48.03
REMARK 500    ASN H 211       29.94     49.89
REMARK 500    ARG C  32     -158.06   -135.79
REMARK 500    SER C  86      -82.78    -70.12
REMARK 500    GLN C  88        3.24     85.23
REMARK 500    GLN C 102     -112.67    123.70
REMARK 500    ARG C 103     -161.83   -126.16
REMARK 500    GLU C 107      135.94     84.72
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 ILE H   56     ASN H   57                 -147.45
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS
REMARK 500    VAL H   2        24.5      L          L   OUTSIDE RANGE
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 H 311        DISTANCE =  5.06 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4G3Z   RELATED DB: PDB
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE SEQUENCE DATABASE REFERENCES FOR CHAIN L, H DO NOT CURRENTLY
REMARK 999 EXIST.
DBREF  4G3Y L    1   214  PDB    4G3Y     4G3Y             1    214
DBREF  4G3Y H    1   226  PDB    4G3Y     4G3Y             1    226
DBREF  4G3Y C    1   157  UNP    P01375   TNFA_HUMAN      77    233
SEQRES   1 L  214  ASP ILE LEU LEU THR GLN SER PRO ALA ILE LEU SER VAL
SEQRES   2 L  214  SER PRO GLY GLU ARG VAL SER PHE SER CYS ARG ALA SER
SEQRES   3 L  214  GLN PHE VAL GLY SER SER ILE HIS TRP TYR GLN GLN ARG
SEQRES   4 L  214  THR ASN GLY SER PRO ARG LEU LEU ILE LYS TYR ALA SER
SEQRES   5 L  214  GLU SER MET SER GLY ILE PRO SER ARG PHE SER GLY SER
SEQRES   6 L  214  GLY SER GLY THR ASP PHE THR LEU SER ILE ASN THR VAL
SEQRES   7 L  214  GLU SER GLU ASP ILE ALA ASP TYR TYR CYS GLN GLN SER
SEQRES   8 L  214  HIS SER TRP PRO PHE THR PHE GLY SER GLY THR ASN LEU
SEQRES   9 L  214  GLU VAL LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE
SEQRES  10 L  214  PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA
SEQRES  11 L  214  SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU
SEQRES  12 L  214  ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER
SEQRES  13 L  214  GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS
SEQRES  14 L  214  ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER
SEQRES  15 L  214  LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU
SEQRES  16 L  214  VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER
SEQRES  17 L  214  PHE ASN ARG GLY GLU CYS
SEQRES   1 H  226  GLU VAL LYS LEU GLU GLU SER GLY GLY GLY LEU VAL GLN
SEQRES   2 H  226  PRO GLY GLY SER MET LYS LEU SER CYS VAL ALA SER GLY
SEQRES   3 H  226  PHE ILE PHE SER ASN HIS TRP MET ASN TRP VAL ARG GLN
SEQRES   4 H  226  SER PRO GLU LYS GLY LEU GLU TRP VAL ALA GLU ILE ARG
SEQRES   5 H  226  SER LYS SER ILE ASN SER ALA THR HIS TYR ALA GLU SER
SEQRES   6 H  226  VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASP SER LYS
SEQRES   7 H  226  SER ALA VAL TYR LEU GLN MET THR ASP LEU ARG THR GLU
SEQRES   8 H  226  ASP THR GLY VAL TYR TYR CYS SER ARG ASN TYR TYR GLY
SEQRES   9 H  226  SER THR TYR ASP TYR TRP GLY GLN GLY THR THR LEU THR
SEQRES  10 H  226  VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO
SEQRES  11 H  226  LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA
SEQRES  12 H  226  ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO
SEQRES  13 H  226  VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY
SEQRES  14 H  226  VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU
SEQRES  15 H  226  TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER
SEQRES  16 H  226  LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS
SEQRES  17 H  226  PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS
SEQRES  18 H  226  SER CYS ASP LYS THR
SEQRES   1 C  157  VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO VAL
SEQRES   2 C  157  ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU
SEQRES   3 C  157  GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN
SEQRES   4 C  157  GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER
SEQRES   5 C  157  GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE LYS
SEQRES   6 C  157  GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS
SEQRES   7 C  157  THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS VAL
SEQRES   8 C  157  ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG GLU
SEQRES   9 C  157  THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU PRO
SEQRES  10 C  157  ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY ASP
SEQRES  11 C  157  ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU ASP
SEQRES  12 C  157  PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA
SEQRES  13 C  157  LEU
FORMUL   4  HOH   *134(H2 O)
HELIX    1   1 GLU L   79  ILE L   83  5                                   5
HELIX    2   2 SER L  121  SER L  127  1                                   7
HELIX    3   3 LYS L  183  GLU L  187  1                                   5
HELIX    4   4 ILE H   28  HIS H   32  5                                   5
HELIX    5   5 SER H   53  ASN H   57  5                                   5
HELIX    6   6 ARG H   89  THR H   93  5                                   5
HELIX    7   7 SER H  163  ALA H  165  5                                   3
HELIX    8   8 SER H  194  GLY H  197  5                                   4
HELIX    9   9 LYS H  208  ASN H  211  5                                   4
HELIX   10  10 ARG C  138  LEU C  142  5                                   5
SHEET    1   A 4 LEU L   4  THR L   5  0
SHEET    2   A 4 VAL L  19  ALA L  25 -1  O  ARG L  24   N  THR L   5
SHEET    3   A 4 ASP L  70  ILE L  75 -1  O  LEU L  73   N  PHE L  21
SHEET    4   A 4 PHE L  62  SER L  67 -1  N  SER L  63   O  SER L  74
SHEET    1   B 6 ILE L  10  VAL L  13  0
SHEET    2   B 6 THR L 102  VAL L 106  1  O  GLU L 105   N  VAL L  13
SHEET    3   B 6 ALA L  84  GLN L  90 -1  N  ALA L  84   O  LEU L 104
SHEET    4   B 6 ILE L  33  GLN L  38 -1  N  HIS L  34   O  GLN L  89
SHEET    5   B 6 ARG L  45  LYS L  49 -1  O  LEU L  47   N  TRP L  35
SHEET    6   B 6 GLU L  53  SER L  54 -1  O  GLU L  53   N  LYS L  49
SHEET    1   C 4 ILE L  10  VAL L  13  0
SHEET    2   C 4 THR L 102  VAL L 106  1  O  GLU L 105   N  VAL L  13
SHEET    3   C 4 ALA L  84  GLN L  90 -1  N  ALA L  84   O  LEU L 104
SHEET    4   C 4 THR L  97  PHE L  98 -1  O  THR L  97   N  GLN L  90
SHEET    1   D 4 SER L 114  PHE L 118  0
SHEET    2   D 4 THR L 129  PHE L 139 -1  O  VAL L 133   N  PHE L 118
SHEET    3   D 4 TYR L 173  SER L 182 -1  O  LEU L 179   N  VAL L 132
SHEET    4   D 4 SER L 159  VAL L 163 -1  N  GLN L 160   O  THR L 178
SHEET    1   E 4 ALA L 144  LYS L 145  0
SHEET    2   E 4 VAL L 191  HIS L 198 -1  O  THR L 197   N  LYS L 145
SHEET    3   E 4 TRP L 148  VAL L 150 -1  N  LYS L 149   O  ALA L 193
SHEET    4   E 4 ALA L 153  LEU L 154 -1  O  ALA L 153   N  VAL L 150
SHEET    1   F 3 ALA L 144  LYS L 145  0
SHEET    2   F 3 VAL L 191  HIS L 198 -1  O  THR L 197   N  LYS L 145
SHEET    3   F 3 VAL L 205  ASN L 210 -1  O  LYS L 207   N  CYS L 194
SHEET    1   G 4 LYS H   3  SER H   7  0
SHEET    2   G 4 MET H  18  SER H  25 -1  O  SER H  21   N  SER H   7
SHEET    3   G 4 ALA H  80  MET H  85 -1  O  MET H  85   N  MET H  18
SHEET    4   G 4 PHE H  70  ASP H  75 -1  N  SER H  73   O  TYR H  82
SHEET    1   H 6 GLY H  10  VAL H  12  0
SHEET    2   H 6 THR H 114  VAL H 118  1  O  THR H 117   N  GLY H  10
SHEET    3   H 6 GLY H  94  ASN H 101 -1  N  TYR H  96   O  THR H 114
SHEET    4   H 6 TRP H  33  SER H  40 -1  N  VAL H  37   O  TYR H  97
SHEET    5   H 6 GLY H  44  ILE H  51 -1  O  GLU H  46   N  ARG H  38
SHEET    6   H 6 THR H  60  TYR H  62 -1  O  HIS H  61   N  GLU H  50
SHEET    1   I 4 GLY H  10  VAL H  12  0
SHEET    2   I 4 THR H 114  VAL H 118  1  O  THR H 117   N  GLY H  10
SHEET    3   I 4 GLY H  94  ASN H 101 -1  N  TYR H  96   O  THR H 114
SHEET    4   I 4 TYR H 107  TRP H 110 -1  O  TYR H 109   N  ARG H 100
SHEET    1   J 4 SER H 127  LEU H 131  0
SHEET    2   J 4 THR H 142  TYR H 152 -1  O  GLY H 146   N  LEU H 131
SHEET    3   J 4 TYR H 183  PRO H 192 -1  O  VAL H 191   N  ALA H 143
SHEET    4   J 4 VAL H 170  THR H 172 -1  N  HIS H 171   O  VAL H 188
SHEET    1   K 4 SER H 127  LEU H 131  0
SHEET    2   K 4 THR H 142  TYR H 152 -1  O  GLY H 146   N  LEU H 131
SHEET    3   K 4 TYR H 183  PRO H 192 -1  O  VAL H 191   N  ALA H 143
SHEET    4   K 4 VAL H 176  LEU H 177 -1  N  VAL H 176   O  SER H 184
SHEET    1   L 3 THR H 158  TRP H 161  0
SHEET    2   L 3 TYR H 201  HIS H 207 -1  O  ASN H 206   N  THR H 158
SHEET    3   L 3 THR H 212  VAL H 214 -1  O  THR H 212   N  HIS H 207
SHEET    1   M 3 THR H 158  TRP H 161  0
SHEET    2   M 3 TYR H 201  HIS H 207 -1  O  ASN H 206   N  THR H 158
SHEET    3   M 3 LYS H 217  VAL H 218 -1  O  VAL H 218   N  TYR H 201
SHEET    1   N 3 TRP C  28  LEU C  29  0
SHEET    2   N 3 VAL C  13  ALA C  18 -1  N  VAL C  17   O  LEU C  29
SHEET    3   N 3 LEU C  36  ALA C  38 -1  O  LEU C  36   N  HIS C  15
SHEET    1   O 5 TRP C  28  LEU C  29  0
SHEET    2   O 5 VAL C  13  ALA C  18 -1  N  VAL C  17   O  LEU C  29
SHEET    3   O 5 TYR C 151  ALA C 156 -1  O  ILE C 154   N  ALA C  14
SHEET    4   O 5 GLY C  54  GLN C  67 -1  N  TYR C  59   O  GLY C 153
SHEET    5   O 5 PRO C 113  LEU C 126 -1  O  GLY C 122   N  ILE C  58
SHEET    1   P 5 GLU C  42  ARG C  44  0
SHEET    2   P 5 GLN C  47  VAL C  49 -1  O  VAL C  49   N  GLU C  42
SHEET    3   P 5 ARG C 131  ILE C 136 -1  O  LEU C 132   N  LEU C  48
SHEET    4   P 5 LEU C  76  ILE C  83 -1  N  THR C  79   O  GLU C 135
SHEET    5   P 5 LYS C  90  LYS C  98 -1  O  LEU C  94   N  ILE C  80
SSBOND   1 CYS L   23    CYS L   88                          1555   1555  2.05
SSBOND   2 CYS L  134    CYS L  194                          1555   1555  2.03
SSBOND   3 CYS H   22    CYS H   98                          1555   1555  2.05
SSBOND   4 CYS H  147    CYS H  203                          1555   1555  2.03
SSBOND   5 CYS C   69    CYS C  101                          1555   1555  2.06
CISPEP   1 SER L    7    PRO L    8          0         2.35
CISPEP   2 TRP L   94    PRO L   95          0         6.74
CISPEP   3 TYR L  140    PRO L  141          0         1.27
CISPEP   4 GLU H    1    VAL H    2          0         3.36
CISPEP   5 GLY H  140    GLY H  141          0         9.68
CISPEP   6 PHE H  153    PRO H  154          0        -3.35
CISPEP   7 GLU H  155    PRO H  156          0         0.91
CISPEP   8 CYS C  101    GLN C  102          0        -3.69
CRYST1  153.663  153.663   99.279  90.00  90.00 120.00 H 3           9
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      0.006508  0.003757  0.000000        0.00000
SCALE2      0.000000  0.007514  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010073        0.00000
      
PROCHECK
Go to PROCHECK summary
 References