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PDBsum entry 3wd5

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Immune system PDB id
3wd5
Jmol
Contents
Protein chains
152 a.a.
213 a.a.
214 a.a.
Waters ×34
HEADER    IMMUNE SYSTEM                           06-JUN-13   3WD5
TITLE     CRYSTAL STRUCTURE OF TNFALPHA IN COMPLEX WITH ADALIMUMAB FAB FRAGMENT
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: TUMOR NECROSIS FACTOR;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: TUMOR NECROSIS FACTOR, SOLUBLE FORM;
COMPND   5 SYNONYM: TNFALPHA;
COMPND   6 ENGINEERED: YES;
COMPND   7 MOL_ID: 2;
COMPND   8 MOLECULE: ADALIMUMAB LIGHT CHAIN;
COMPND   9 CHAIN: L;
COMPND  10 ENGINEERED: YES;
COMPND  11 MOL_ID: 3;
COMPND  12 MOLECULE: ADALIMUMAB HEAVY CHAIN;
COMPND  13 CHAIN: H;
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 GENE: TNFA;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 MOL_ID: 2;
SOURCE   9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE  10 ORGANISM_COMMON: HUMAN;
SOURCE  11 ORGANISM_TAXID: 9606;
SOURCE  12 EXPRESSION_SYSTEM: CRICETULUS GRISEUS;
SOURCE  13 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER;
SOURCE  14 EXPRESSION_SYSTEM_TAXID: 10029;
SOURCE  15 MOL_ID: 3;
SOURCE  16 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE  17 ORGANISM_COMMON: HUMAN;
SOURCE  18 ORGANISM_TAXID: 9606;
SOURCE  19 EXPRESSION_SYSTEM: CRICETULUS GRISEUS;
SOURCE  20 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER;
SOURCE  21 EXPRESSION_SYSTEM_TAXID: 10029
KEYWDS    ANTIBODY BINDING EPITOPE, IMMUNE SYSTEM
EXPDTA    X-RAY DIFFRACTION
AUTHOR    S.HU,S.Y.LIANG,Y.J.GUO,Z.Y.LOU
REVDAT   2   21-AUG-13 3WD5    1       JRNL
REVDAT   1   14-AUG-13 3WD5    0
JRNL        AUTH   S.HU,S.Y.LIANG,H.GUO,D.ZHANG,H.LI,X.WANG,W.YANG,W.QIAN,
JRNL        AUTH 2 S.HOU,H.WANG,Y.J.GUO,Z.Y.LOU
JRNL        TITL   COMPARISON OF THE INHIBITION MECHANISMS OF ADALIMUMAB AND
JRNL        TITL 2 INFLIXIMAB IN TREATING TNFALPHA-ASSOCIATED DISEASES FROM A
JRNL        TITL 3 MOLECULAR VIEW
JRNL        REF    J.BIOL.CHEM.                               2013
JRNL        REFN                   ESSN 1083-351X
JRNL        DOI    10.1074/JBC.M113.491530
REMARK   2
REMARK   2 RESOLUTION.    3.10 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.8.1_1168)
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) : 3.10
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 43.26
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.9
REMARK   3   NUMBER OF REFLECTIONS             : 12943
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) : 0.187
REMARK   3   FREE R VALUE                     : 0.275
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.990
REMARK   3   FREE R VALUE TEST SET COUNT      : 646
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 43.2602 -  5.3001    1.00     2544   130  0.2131 0.2585
REMARK   3     2  5.3001 -  4.2080    1.00     2462   124  0.1554 0.2313
REMARK   3     3  4.2080 -  3.6764    1.00     2429   138  0.1705 0.2515
REMARK   3     4  3.6764 -  3.3404    1.00     2440   121  0.1899 0.3576
REMARK   3     5  3.3404 -  3.1010    1.00     2422   133  0.2119 0.3461
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              : NULL
REMARK   3   B_SOL              : NULL
REMARK   3
REMARK   3  ERROR ESTIMATES.
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.420
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.200
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 49.23
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 48.06
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
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      :  0.010           4536
REMARK   3   ANGLE     :  1.447           6168
REMARK   3   CHIRALITY :  0.113            697
REMARK   3   PLANARITY :  0.006            795
REMARK   3   DIHEDRAL  : 17.883           1630
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 3WD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUN-13.
REMARK 100 THE RCSB ID CODE IS RCSB096185.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : NULL
REMARK 200  PH                             : 4.6
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
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : NULL
REMARK 200  DETECTOR MANUFACTURER          : NULL
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 12943
REMARK 200  RESOLUTION RANGE HIGH      (A) : 3.100
REMARK 200  RESOLUTION RANGE LOW       (A) : 43.300
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 26.100
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 100.0
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: PHASES
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 55.48
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG400, 0.1M SODIUM ACETATE
REMARK 280  TRIHYDRATE, 0.1M CADMIUM CHLORIDE HYDRATE, PH 4.6, VAPOR
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 291.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3
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       5555   Z,X,Y
REMARK 290       6555   Z+1/2,-X+1/2,-Y
REMARK 290       7555   -Z+1/2,-X,Y+1/2
REMARK 290       8555   -Z,X+1/2,-Y+1/2
REMARK 290       9555   Y,Z,X
REMARK 290      10555   -Y,Z+1/2,-X+1/2
REMARK 290      11555   Y+1/2,-Z+1/2,-X
REMARK 290      12555   -Y+1/2,-Z,X+1/2
REMARK 290      13555   X+1/2,Y+1/2,Z+1/2
REMARK 290      14555   -X,-Y+1/2,Z
REMARK 290      15555   -X+1/2,Y,-Z
REMARK 290      16555   X,-Y,-Z+1/2
REMARK 290      17555   Z+1/2,X+1/2,Y+1/2
REMARK 290      18555   Z,-X,-Y+1/2
REMARK 290      19555   -Z,-X+1/2,Y
REMARK 290      20555   -Z+1/2,X,-Y
REMARK 290      21555   Y+1/2,Z+1/2,X+1/2
REMARK 290      22555   -Y+1/2,Z,-X
REMARK 290      23555   Y,-Z,-X+1/2
REMARK 290      24555   -Y,-Z+1/2,X
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       80.92450
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       80.92450
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       80.92450
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       80.92450
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       80.92450
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   5  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY2   5  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   5  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY1   6  0.000000  0.000000  1.000000       80.92450
REMARK 290   SMTRY2   6 -1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY3   6  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY1   7  0.000000  0.000000 -1.000000       80.92450
REMARK 290   SMTRY2   7 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  1.000000  0.000000       80.92450
REMARK 290   SMTRY1   8  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY2   8  1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY3   8  0.000000 -1.000000  0.000000       80.92450
REMARK 290   SMTRY1   9  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   9  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY3   9  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY1  10  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2  10  0.000000  0.000000  1.000000       80.92450
REMARK 290   SMTRY3  10 -1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY1  11  0.000000  1.000000  0.000000       80.92450
REMARK 290   SMTRY2  11  0.000000  0.000000 -1.000000       80.92450
REMARK 290   SMTRY3  11 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY1  12  0.000000 -1.000000  0.000000       80.92450
REMARK 290   SMTRY2  12  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY3  12  1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY1  13  1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY2  13  0.000000  1.000000  0.000000       80.92450
REMARK 290   SMTRY3  13  0.000000  0.000000  1.000000       80.92450
REMARK 290   SMTRY1  14 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2  14  0.000000 -1.000000  0.000000       80.92450
REMARK 290   SMTRY3  14  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1  15 -1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY2  15  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3  15  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1  16  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2  16  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3  16  0.000000  0.000000 -1.000000       80.92450
REMARK 290   SMTRY1  17  0.000000  0.000000  1.000000       80.92450
REMARK 290   SMTRY2  17  1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY3  17  0.000000  1.000000  0.000000       80.92450
REMARK 290   SMTRY1  18  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY2  18 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3  18  0.000000 -1.000000  0.000000       80.92450
REMARK 290   SMTRY1  19  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY2  19 -1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY3  19  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY1  20  0.000000  0.000000 -1.000000       80.92450
REMARK 290   SMTRY2  20  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3  20  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY1  21  0.000000  1.000000  0.000000       80.92450
REMARK 290   SMTRY2  21  0.000000  0.000000  1.000000       80.92450
REMARK 290   SMTRY3  21  1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY1  22  0.000000 -1.000000  0.000000       80.92450
REMARK 290   SMTRY2  22  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY3  22 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY1  23  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2  23  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY3  23 -1.000000  0.000000  0.000000       80.92450
REMARK 290   SMTRY1  24  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2  24  0.000000  0.000000 -1.000000       80.92450
REMARK 290   SMTRY3  24  1.000000  0.000000  0.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L, H
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 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 201  LIES ON A SPECIAL POSITION.
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     VAL A     1
REMARK 465     ARG A     2
REMARK 465     SER A     3
REMARK 465     SER A     4
REMARK 465     SER A     5
REMARK 465     LYS H   137
REMARK 465     SER H   138
REMARK 465     THR H   139
REMARK 465     SER H   140
REMARK 465     GLY H   141
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480   M RES C SSEQI ATOMS
REMARK 480     LYS L   45   CE
REMARK 480     GLU L   81   CG
REMARK 480     GLN L  100   CG
REMARK 480     LYS L  126   CE   NZ
REMARK 480     GLN L  147   CG
REMARK 480     LEU L  154   CD1  CD2
REMARK 480     LYS L  169   CG   CD   CE
REMARK 480     LYS L  188   NZ
REMARK 480     ARG L  211   NH2
REMARK 480     GLY L  212   CA
REMARK 480     GLU L  213   CA   O    CB   CG
REMARK 480     GLU H    1   OE2
REMARK 480     PRO H   41   CA
REMARK 480     GLU H   89   CG
REMARK 480     SER H  135   CA   CB
REMARK 480     SER H  136   CB
REMARK 480     GLY H  142   CA
REMARK 480     SER H  196   N
REMARK 480     GLY H  198   CA
REMARK 480     LYS H  209   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   SG   CYS A    69     CB   CYS A   101              1.75
REMARK 500   OD2  ASP H    59     O    HOH H   303              2.06
REMARK 500   O    ALA A   145     O    HOH H   303              2.07
REMARK 500   OD1  ASP H    30     O    HOH H   305              2.15
REMARK 500   O    ALA H    61     N    SER H    63              2.17
REMARK 500   O    VAL H    64     N    GLY H    66              2.18
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    SER A   9      130.77     95.62
REMARK 500    ALA A  33     -137.08     22.15
REMARK 500    LEU A  37       88.08   -179.36
REMARK 500    ARG A  44      -68.46   -126.68
REMARK 500    ASP A  45       47.82   -106.53
REMARK 500    PRO A  70     -126.32   -106.35
REMARK 500    THR A  72      -46.51      3.53
REMARK 500    SER A  86      -72.99    -86.94
REMARK 500    TYR A  87       80.09    -57.98
REMARK 500    GLN A  88        2.89    -56.83
REMARK 500    ALA A  96      135.95   -175.10
REMARK 500    CYS A 101      104.28      2.31
REMARK 500    ARG A 103      -29.13     41.98
REMARK 500    GLU A 104      -51.90     -4.51
REMARK 500    THR A 105       79.92     37.57
REMARK 500    PRO A 106       49.56    -60.27
REMARK 500    ALA A 109     -173.70   -170.26
REMARK 500    GLU A 110      121.31     69.19
REMARK 500    SER A 147      -79.11    -52.47
REMARK 500    ILE L   2      124.98     75.57
REMARK 500    ARG L  30     -124.49     54.88
REMARK 500    ALA L  51      -30.92     72.77
REMARK 500    SER L  52      -16.77   -140.13
REMARK 500    SER L  77       88.36   -156.66
REMARK 500    ARG L  93      109.62     81.01
REMARK 500    LYS L 107      -89.34    -55.22
REMARK 500    ARG L 108      157.97     30.26
REMARK 500    ASN L 152       14.61     59.68
REMARK 500    ARG H  16     -150.90    -76.16
REMARK 500    ASP H  62       62.12    -43.87
REMARK 500    SER H  63       -8.42    173.48
REMARK 500    VAL H  64      -72.84   -142.46
REMARK 500    GLU H  65      -61.81     35.11
REMARK 500    ARG H  72      114.11   -165.64
REMARK 500    LEU H 102      -81.51     57.26
REMARK 500    ALA H 122     -142.34    -70.77
REMARK 500    ASP H 152       62.54     60.64
REMARK 500    ALA H 166       15.92    -59.81
REMARK 500    LEU H 167      109.15   -160.68
REMARK 500    SER H 194       -6.73    -54.63
REMARK 500    SER H 195      -60.70   -103.32
REMARK 500    SER H 196       45.68    -59.03
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    ASN L  92        16.6      L          L   OUTSIDE RANGE
REMARK 500    ARG L  93        16.3      L          L   OUTSIDE RANGE
REMARK 500    ARG L 108        24.2      L          L   OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4G3Y   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF TNFALPHA IN COMPLEX WITH INFLIXIMAB
REMARK 900 FAB FRAGMENT
DBREF  3WD5 A    1   157  UNP    P01375   TNFA_HUMAN      77    233
DBREF  3WD5 L    1   213  PDB    3WD5     3WD5             1    213
DBREF  3WD5 H    1   219  PDB    3WD5     3WD5             1    219
SEQADV 3WD5 ASP A   31  UNP  P01375    ARG   107 CONFLICT
SEQRES   1 A  157  VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO VAL
SEQRES   2 A  157  ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU
SEQRES   3 A  157  GLN TRP LEU ASN ASP ARG ALA ASN ALA LEU LEU ALA ASN
SEQRES   4 A  157  GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER
SEQRES   5 A  157  GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE LYS
SEQRES   6 A  157  GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS
SEQRES   7 A  157  THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS VAL
SEQRES   8 A  157  ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG GLU
SEQRES   9 A  157  THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU PRO
SEQRES  10 A  157  ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY ASP
SEQRES  11 A  157  ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU ASP
SEQRES  12 A  157  PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA
SEQRES  13 A  157  LEU
SEQRES   1 L  213  ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA
SEQRES   2 L  213  SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER
SEQRES   3 L  213  GLN GLY ILE ARG ASN TYR LEU ALA TRP TYR GLN GLN LYS
SEQRES   4 L  213  PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER
SEQRES   5 L  213  THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER
SEQRES   6 L  213  GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU
SEQRES   7 L  213  GLN PRO GLU ASP VAL ALA THR TYR TYR CYS GLN ARG TYR
SEQRES   8 L  213  ASN ARG ALA PRO TYR THR PHE GLY GLN GLY THR LYS VAL
SEQRES   9 L  213  GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE
SEQRES  10 L  213  PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA
SEQRES  11 L  213  SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU
SEQRES  12 L  213  ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER
SEQRES  13 L  213  GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS
SEQRES  14 L  213  ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER
SEQRES  15 L  213  LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU
SEQRES  16 L  213  VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER
SEQRES  17 L  213  PHE ASN ARG GLY GLU
SEQRES   1 H  219  GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN
SEQRES   2 H  219  PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY
SEQRES   3 H  219  PHE THR PHE ASP ASP TYR ALA MET HIS TRP VAL ARG GLN
SEQRES   4 H  219  ALA PRO GLY LYS GLY LEU GLU TRP VAL SER ALA ILE THR
SEQRES   5 H  219  TRP ASN SER GLY HIS ILE ASP TYR ALA ASP SER VAL GLU
SEQRES   6 H  219  GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER
SEQRES   7 H  219  LEU TYR LEU ASP MET ASN SER LEU ARG ALA GLU ASP THR
SEQRES   8 H  219  ALA VAL TYR TYR CYS ALA LYS VAL SER TYR LEU SER THR
SEQRES   9 H  219  ALA SER SER LEU ASP TYR TRP GLY GLN GLY THR LEU VAL
SEQRES  10 H  219  THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE
SEQRES  11 H  219  PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR
SEQRES  12 H  219  ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU
SEQRES  13 H  219  PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER
SEQRES  14 H  219  GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY
SEQRES  15 H  219  LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER
SEQRES  16 H  219  SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS
SEQRES  17 H  219  LYS PRO SER ASN THR LYS VAL ASP LYS LYS ILE
FORMUL   4  HOH   *34(H2 O)
HELIX    1   1 ARG A  138  LEU A  142  5                                   5
HELIX    2   2 GLU A  146  GLN A  149  5                                   4
HELIX    3   3 GLN L   79  VAL L   83  5                                   5
HELIX    4   4 SER L  121  GLY L  128  1                                   8
HELIX    5   5 LYS L  183  GLU L  187  1                                   5
HELIX    6   6 THR H   28  TYR H   32  5                                   5
HELIX    7   7 ARG H   87  THR H   91  5                                   5
HELIX    8   8 SER H  164  ALA H  166  5                                   3
SHEET    1   A 3 TRP A  28  LEU A  29  0
SHEET    2   A 3 VAL A  13  ALA A  18 -1  N  VAL A  17   O  LEU A  29
SHEET    3   A 3 LEU A  36  ALA A  38 -1  O  ALA A  38   N  VAL A  13
SHEET    1   B 5 TRP A  28  LEU A  29  0
SHEET    2   B 5 VAL A  13  ALA A  18 -1  N  VAL A  17   O  LEU A  29
SHEET    3   B 5 TYR A 151  LEU A 157 -1  O  PHE A 152   N  VAL A  16
SHEET    4   B 5 GLY A  54  GLN A  67 -1  N  TYR A  59   O  GLY A 153
SHEET    5   B 5 PRO A 113  LEU A 126 -1  O  TRP A 114   N  GLY A  66
SHEET    1   C 5 GLU A  42  LEU A  43  0
SHEET    2   C 5 LEU A  48  VAL A  49 -1  O  VAL A  49   N  GLU A  42
SHEET    3   C 5 ARG A 131  ILE A 136 -1  O  LEU A 132   N  LEU A  48
SHEET    4   C 5 LEU A  76  ILE A  83 -1  N  ILE A  83   O  ARG A 131
SHEET    5   C 5 LYS A  90  LYS A  98 -1  O  LEU A  93   N  ILE A  80
SHEET    1   D 4 MET L   4  SER L   7  0
SHEET    2   D 4 VAL L  19  ALA L  25 -1  O  THR L  22   N  SER L   7
SHEET    3   D 4 ASP L  70  ILE L  75 -1  O  LEU L  73   N  ILE L  21
SHEET    4   D 4 PHE L  62  SER L  63 -1  N  SER L  63   O  THR L  74
SHEET    1   E 6 SER L  10  ALA L  13  0
SHEET    2   E 6 THR L 102  ILE L 106  1  O  GLU L 105   N  LEU L  11
SHEET    3   E 6 THR L  85  ARG L  90 -1  N  TYR L  86   O  THR L 102
SHEET    4   E 6 LEU L  33  GLN L  38 -1  N  TYR L  36   O  TYR L  87
SHEET    5   E 6 LYS L  45  TYR L  49 -1  O  LYS L  45   N  GLN L  37
SHEET    6   E 6 THR L  53  LEU L  54 -1  O  THR L  53   N  TYR L  49
SHEET    1   F 3 SER L 114  PHE L 118  0
SHEET    2   F 3 THR L 129  PHE L 139 -1  O  LEU L 135   N  PHE L 116
SHEET    3   F 3 TYR L 173  SER L 182 -1  O  TYR L 173   N  PHE L 139
SHEET    1   G 4 ALA L 153  LEU L 154  0
SHEET    2   G 4 LYS L 145  VAL L 150 -1  N  VAL L 150   O  ALA L 153
SHEET    3   G 4 VAL L 191  THR L 197 -1  O  ALA L 193   N  LYS L 149
SHEET    4   G 4 VAL L 205  ASN L 210 -1  O  VAL L 205   N  VAL L 196
SHEET    1   H 4 GLN H   3  SER H   7  0
SHEET    2   H 4 LEU H  18  SER H  25 -1  O  SER H  21   N  SER H   7
SHEET    3   H 4 SER H  78  MET H  83 -1  O  MET H  83   N  LEU H  18
SHEET    4   H 4 PHE H  68  ASP H  73 -1  N  SER H  71   O  TYR H  80
SHEET    1   I 6 GLY H  10  VAL H  12  0
SHEET    2   I 6 LEU H 116  VAL H 119  1  O  THR H 118   N  GLY H  10
SHEET    3   I 6 ALA H  92  VAL H  99 -1  N  ALA H  92   O  VAL H 117
SHEET    4   I 6 MET H  34  GLN H  39 -1  N  VAL H  37   O  TYR H  95
SHEET    5   I 6 LEU H  45  ILE H  51 -1  O  SER H  49   N  TRP H  36
SHEET    6   I 6 ILE H  58  TYR H  60 -1  O  ASP H  59   N  ALA H  50
SHEET    1   J 4 GLY H  10  VAL H  12  0
SHEET    2   J 4 LEU H 116  VAL H 119  1  O  THR H 118   N  GLY H  10
SHEET    3   J 4 ALA H  92  VAL H  99 -1  N  ALA H  92   O  VAL H 117
SHEET    4   J 4 LEU H 108  TRP H 111 -1  O  TYR H 110   N  LYS H  98
SHEET    1   K 4 SER H 128  LEU H 132  0
SHEET    2   K 4 THR H 143  TYR H 153 -1  O  GLY H 147   N  LEU H 132
SHEET    3   K 4 TYR H 184  PRO H 193 -1  O  VAL H 190   N  LEU H 146
SHEET    4   K 4 VAL H 171  THR H 173 -1  N  HIS H 172   O  VAL H 189
SHEET    1   L 4 SER H 128  LEU H 132  0
SHEET    2   L 4 THR H 143  TYR H 153 -1  O  GLY H 147   N  LEU H 132
SHEET    3   L 4 TYR H 184  PRO H 193 -1  O  VAL H 190   N  LEU H 146
SHEET    4   L 4 VAL H 177  LEU H 178 -1  N  VAL H 177   O  SER H 185
SHEET    1   M 3 THR H 159  TRP H 162  0
SHEET    2   M 3 TYR H 202  HIS H 208 -1  O  ASN H 207   N  THR H 159
SHEET    3   M 3 THR H 213  VAL H 215 -1  O  THR H 213   N  HIS H 208
SHEET    1   N 3 THR H 159  TRP H 162  0
SHEET    2   N 3 TYR H 202  HIS H 208 -1  O  ASN H 207   N  THR H 159
SHEET    3   N 3 LYS H 218  ILE H 219 -1  O  ILE H 219   N  TYR H 202
SSBOND   1 CYS A   69    CYS A  101                          1555   1555  2.05
SSBOND   2 CYS L   23    CYS L   88                          1555   1555  2.06
SSBOND   3 CYS L  134    CYS L  194                          1555   1555  2.04
SSBOND   4 CYS H   22    CYS H   96                          1555   1555  2.05
SSBOND   5 CYS H  148    CYS H  204                          1555   1555  2.03
CISPEP   1 ARG A    6    THR A    7          0        13.50
CISPEP   2 SER L    7    PRO L    8          0        -2.24
CISPEP   3 ASN L   92    ARG L   93          0        -5.94
CISPEP   4 ALA L   94    PRO L   95          0        -4.86
CISPEP   5 TYR L  140    PRO L  141          0         5.44
CISPEP   6 PHE H  154    PRO H  155          0        -4.04
CISPEP   7 GLU H  156    PRO H  157          0         3.57
CRYST1  161.849  161.849  161.849  90.00  90.00  90.00 I 21 3       24
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      0.006179  0.000000  0.000000        0.00000
SCALE2      0.000000  0.006179  0.000000        0.00000
SCALE3      0.000000  0.000000  0.006179        0.00000
      
PROCHECK
Go to PROCHECK summary
 References