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PDBsum entry 2zpx

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Cytokine PDB id
2zpx
Jmol
Contents
Protein chains
142 a.a.
Waters ×7
HEADER    CYTOKINE                                29-JUL-08   2ZPX
TITLE     TNF RECEPTOR SUBTYPE ONE-SELECTIVE TNF MUTANT WITH
TITLE    2 ANTAGONISTIC ACTIVITY; R1ANTTNF-T8
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: TUMOR NECROSIS FACTOR;
COMPND   3 CHAIN: A, B, C;
COMPND   4 FRAGMENT: UNP RESIDUES 77-233;
COMPND   5 SYNONYM: TNF-ALPHA, TUMOR NECROSIS FACTOR LIGAND
COMPND   6 SUPERFAMILY MEMBER 2, TNF-A, CACHECTIN, ANTAGONISTIC TNF
COMPND   7 MUTANT (R1ANTTNF-T8);
COMPND   8 ENGINEERED: YES;
COMPND   9 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 STRAIN: HUMAN;
SOURCE   6 GENE: TNF, TNFA, TNFSF2;
SOURCE   7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE  10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  11 EXPRESSION_SYSTEM_PLASMID: PYAS(MODIFIED FROM PUC18)
KEYWDS    TUMOR NECROSIS FACTOR, TRIMER, ANTAGONISTIC ACTIVITY, TNFR1
KEYWDS   2 SPECIFIC, PHAGE DISPLAY SYSTEM, CYTOKINE, CELL MEMBRANE,
KEYWDS   3 LIPOPROTEIN, MEMBRANE, MYRISTATE, PHOSPHOPROTEIN,
KEYWDS   4 POLYMORPHISM, SECRETED, SIGNAL-ANCHOR, TRANSMEMBRANE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    Y.MUKAI,T.NAKAMURA,Y.YAMAGATA,Y.TSUTSUMI
REVDAT   2   18-AUG-09 2ZPX    1       JRNL
REVDAT   1   24-MAR-09 2ZPX    0
JRNL        AUTH   Y.MUKAI,T.NAKAMURA,Y.YOSHIOKA,H.SHIBATA,Y.ABE,
JRNL        AUTH 2 T.NOMURA,M.TANIAI,T.OHTA,S.NAKAGAWA,S.TSUNODA,
JRNL        AUTH 3 H.KAMADA,Y.YAMAGATA,Y.TSUTSUMI
JRNL        TITL   FAST BINDING KINETICS AND CONSERVED 3D STRUCTURE
JRNL        TITL 2 UNDERLIE THE ANTAGONISTIC ACTIVITY OF MUTANT TNF:
JRNL        TITL 3 USEFUL INFORMATION FOR DESIGNING ARTIFICIAL
JRNL        TITL 4 PROTEO-ANTAGONISTS
JRNL        REF    J.BIOCHEM.                    V. 146   167 2009
JRNL        REFN                   ISSN 0021-924X
JRNL        PMID   19386778
JRNL        DOI    10.1093/JB/MVP065
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    2.83 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS 1.2
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : NULL
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.83
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 50.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 1361839.840
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 93.2
REMARK   3   NUMBER OF REFLECTIONS             : 9762
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 SET) : 0.268
REMARK   3   FREE R VALUE                     : 0.309
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.300
REMARK   3   FREE R VALUE TEST SET COUNT      : 1009
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.010
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 6
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.80
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.98
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 68.30
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1084
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3400
REMARK   3   BIN FREE R VALUE                    : 0.3840
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 10.00
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 121
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.035
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3312
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 7
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 63.40
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 76.30
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 3.20000
REMARK   3    B22 (A**2) : 3.84000
REMARK   3    B33 (A**2) : -7.04000
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.45
REMARK   3   ESD FROM SIGMAA              (A) : 0.56
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.58
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.77
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.012
REMARK   3   BOND ANGLES            (DEGREES) : 1.90
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 25.50
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.70
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : FLAT MODEL
REMARK   3   KSOL        : 0.15
REMARK   3   BSOL        : 80.28
REMARK   3
REMARK   3  NCS MODEL : CONSTR
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : PROTEIN_REP.PARAM
REMARK   3  PARAMETER FILE  2  : WATER_REP.PARAM
REMARK   3  PARAMETER FILE  3  : NULL
REMARK   3  TOPOLOGY FILE  1   : PROTEIN.TOP
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP
REMARK   3  TOPOLOGY FILE  3   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK   4
REMARK   4 2ZPX COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-08.
REMARK 100 THE RCSB ID CODE IS RCSB028277.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 06-NOV-04
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 6.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : SPRING-8
REMARK 200  BEAMLINE                       : BL41XU
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : NULL
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
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   : 10337
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.800
REMARK 200  RESOLUTION RANGE LOW       (A) : 55.670
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.9
REMARK 200  DATA REDUNDANCY                : 3.500
REMARK 200  R MERGE                    (I) : 0.24400
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 36.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.90
REMARK 200  COMPLETENESS FOR SHELL     (%) : 85.6
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.20
REMARK 200  R MERGE FOR SHELL          (I) : 0.53000
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 3.160
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 1TNF
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 38.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG1500, 0.2M CALCIUM ACETATE,
REMARK 280  0.1M SODIUM CACODYLATE, PH6.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280  TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X+1/2,-Y,Z+1/2
REMARK 290       3555   -X,Y+1/2,-Z+1/2
REMARK 290       4555   X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       24.79300
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       37.69100
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       55.66550
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       37.69100
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       24.79300
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       55.66550
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6520 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17770 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.4 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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     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     ARG A     6
REMARK 465     THR A     7
REMARK 465     ARG A   103
REMARK 465     GLU A   104
REMARK 465     THR A   105
REMARK 465     PRO A   106
REMARK 465     GLU A   107
REMARK 465     GLY A   108
REMARK 465     ALA A   109
REMARK 465     GLU A   110
REMARK 465     VAL B     1
REMARK 465     ARG B     2
REMARK 465     SER B     3
REMARK 465     SER B     4
REMARK 465     SER B     5
REMARK 465     ARG B     6
REMARK 465     THR B     7
REMARK 465     ARG B   103
REMARK 465     GLU B   104
REMARK 465     THR B   105
REMARK 465     PRO B   106
REMARK 465     GLU B   107
REMARK 465     GLY B   108
REMARK 465     ALA B   109
REMARK 465     GLU B   110
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     ARG C   103
REMARK 465     GLU C   104
REMARK 465     THR C   105
REMARK 465     PRO C   106
REMARK 465     GLU C   107
REMARK 465     GLY C   108
REMARK 465     ALA C   109
REMARK 465     GLU C   110
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   NE2  GLN A    21     NH2  ARG C    31     2554     1.83
REMARK 500   NH2  ARG B    32     OD1  ASP C    10     4445     2.00
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    ARG B  32   N     ARG B  32   CA     -0.188
REMARK 500    ASN C  34   CB    ASN C  34   CG     -0.242
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    ARG B  31   CA  -  C   -  N   ANGL. DEV. = -14.6 DEGREES
REMARK 500    ALA B  33   N   -  CA  -  CB  ANGL. DEV. = -10.1 DEGREES
REMARK 500    ALA B  33   N   -  CA  -  C   ANGL. DEV. =  41.6 DEGREES
REMARK 500    ALA B  33   C   -  N   -  CA  ANGL. DEV. = -23.6 DEGREES
REMARK 500    ASN B  34   CB  -  CA  -  C   ANGL. DEV. =  15.1 DEGREES
REMARK 500    ASN B  34   N   -  CA  -  CB  ANGL. DEV. =  15.6 DEGREES
REMARK 500    ALA B  33   CA  -  C   -  N   ANGL. DEV. = -23.4 DEGREES
REMARK 500    ALA B  33   O   -  C   -  N   ANGL. DEV. =  10.7 DEGREES
REMARK 500    ARG C  32   N   -  CA  -  CB  ANGL. DEV. = -11.2 DEGREES
REMARK 500    ARG C  32   C   -  N   -  CA  ANGL. DEV. = -21.0 DEGREES
REMARK 500    ALA C  33   C   -  N   -  CA  ANGL. DEV. = -16.9 DEGREES
REMARK 500    ASN C  34   N   -  CA  -  CB  ANGL. DEV. =  31.3 DEGREES
REMARK 500    ASN C  34   N   -  CA  -  C   ANGL. DEV. = -21.9 DEGREES
REMARK 500    ASN C  34   C   -  N   -  CA  ANGL. DEV. = -20.0 DEGREES
REMARK 500    ALA C  35   N   -  CA  -  C   ANGL. DEV. = -32.0 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    ASP A  10      -53.09   -169.32
REMARK 500    HIS A  15       72.02   -152.99
REMARK 500    GLU A  23       90.53    -43.85
REMARK 500    ASN A  30      -36.90   -130.94
REMARK 500    ARG A  31       79.73    -62.23
REMARK 500    ALA A  33      -75.44    -41.78
REMARK 500    ASN A  34       38.52    -92.82
REMARK 500    LEU A  37       81.11    172.05
REMARK 500    PRO A  51      -75.97    -83.97
REMARK 500    GLN A  67       76.16   -107.10
REMARK 500    SER A  71      -76.43   -145.32
REMARK 500    THR A  72       -4.17    175.04
REMARK 500    HIS A  73       59.67    -93.62
REMARK 500    ALA A  86      -78.79    -64.01
REMARK 500    ASN A  92       95.07    -64.18
REMARK 500    CYS A 101      175.56    -58.06
REMARK 500    ASN A 112       79.07     64.46
REMARK 500    PRO A 139        7.79    -68.41
REMARK 500    ALA A 145      -70.46    -63.42
REMARK 500    HIS B  15       73.73   -153.11
REMARK 500    ALA B  22       30.22    -80.60
REMARK 500    GLU B  23       89.90    -45.27
REMARK 500    ARG B  32     -139.10    -52.84
REMARK 500    ASN B  34        4.48   -165.46
REMARK 500    LEU B  37       81.89    172.92
REMARK 500    PRO B  51      -74.79    -83.38
REMARK 500    SER B  60      149.36   -172.53
REMARK 500    GLN B  67       76.41   -106.91
REMARK 500    SER B  71      -77.30   -145.03
REMARK 500    THR B  72       -3.29    175.47
REMARK 500    HIS B  73       59.54    -94.18
REMARK 500    ALA B  86      -94.51    -54.35
REMARK 500    ASN B  88       42.32    -84.79
REMARK 500    PRO B  90      170.15    -56.55
REMARK 500    VAL B  91      105.97   -161.14
REMARK 500    PRO B 139       18.14    -66.12
REMARK 500    LEU B 142      103.53    -47.58
REMARK 500    SER C   9     -144.63   -157.67
REMARK 500    ASP C  10     -106.13    -59.35
REMARK 500    HIS C  15       71.43   -154.16
REMARK 500    GLU C  23       89.85    -44.47
REMARK 500    ASN C  30       71.42   -105.27
REMARK 500    ARG C  31     -139.25    -84.54
REMARK 500    LEU C  37       82.57    172.06
REMARK 500    PRO C  51      -74.84    -83.98
REMARK 500    SER C  60      148.78   -176.16
REMARK 500    GLN C  67       76.36   -106.95
REMARK 500    SER C  71      -77.25   -144.54
REMARK 500    THR C  72       -2.65    175.11
REMARK 500    HIS C  73       59.05    -94.38
REMARK 500    ILE C  87     -165.77   -101.27
REMARK 500    ASN C  88       38.92   -156.05
REMARK 500    ASN C  92       96.48    -66.17
REMARK 500    CYS C 101     -156.78    -63.51
REMARK 500    ASN C 112       78.89   -151.59
REMARK 500    ARG C 138       78.65   -118.97
REMARK 500    PRO C 139       14.70    -68.60
REMARK 500    PHE C 144       23.88   -174.13
REMARK 500    ALA C 145       29.98    -70.41
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 ARG B   32     ALA B   33                 -139.62
REMARK 500 ALA B   33     ASN B   34                  138.14
REMARK 500 ALA C   33     ASN C   34                  126.59
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, 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    ALA C  33         14.96
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 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: (11X,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     ARG B  32        18.3      L          L   OUTSIDE RANGE
REMARK 500     ALA B  33         5.9      L          D   EXPECTING SP3
REMARK 500     ASN B  34         1.2      L          D   EXPECTING SP3
REMARK 500     ALA C  35        50.0      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 C 159        DISTANCE =  5.20 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1TNF   RELATED DB: PDB
REMARK 900 RELATED ID: 1TNR   RELATED DB: PDB
REMARK 900 RELATED ID: 2EA7   RELATED DB: PDB
REMARK 900 RELATED ID: 2ZJC   RELATED DB: PDB
DBREF  2ZPX A    1   157  UNP    P01375   TNFA_HUMAN      77    233
DBREF  2ZPX B    1   157  UNP    P01375   TNFA_HUMAN      77    233
DBREF  2ZPX C    1   157  UNP    P01375   TNFA_HUMAN      77    233
SEQADV 2ZPX MET A   11  UNP  P01375    LYS    87 ENGINEERED
SEQADV 2ZPX SER A   65  UNP  P01375    LYS   141 ENGINEERED
SEQADV 2ZPX THR A   84  UNP  P01375    ALA   160 ENGINEERED
SEQADV 2ZPX PRO A   85  UNP  P01375    VAL   161 ENGINEERED
SEQADV 2ZPX ALA A   86  UNP  P01375    SER   162 ENGINEERED
SEQADV 2ZPX ILE A   87  UNP  P01375    TYR   163 ENGINEERED
SEQADV 2ZPX ASN A   88  UNP  P01375    GLN   164 ENGINEERED
SEQADV 2ZPX ARG A   89  UNP  P01375    THR   165 ENGINEERED
SEQADV 2ZPX PRO A   90  UNP  P01375    LYS   166 ENGINEERED
SEQADV 2ZPX ARG A   98  UNP  P01375    LYS   174 ENGINEERED
SEQADV 2ZPX ASN A  112  UNP  P01375    LYS   188 ENGINEERED
SEQADV 2ZPX PRO A  128  UNP  P01375    LYS   204 ENGINEERED
SEQADV 2ZPX MET B   11  UNP  P01375    LYS    87 ENGINEERED
SEQADV 2ZPX SER B   65  UNP  P01375    LYS   141 ENGINEERED
SEQADV 2ZPX THR B   84  UNP  P01375    ALA   160 ENGINEERED
SEQADV 2ZPX PRO B   85  UNP  P01375    VAL   161 ENGINEERED
SEQADV 2ZPX ALA B   86  UNP  P01375    SER   162 ENGINEERED
SEQADV 2ZPX ILE B   87  UNP  P01375    TYR   163 ENGINEERED
SEQADV 2ZPX ASN B   88  UNP  P01375    GLN   164 ENGINEERED
SEQADV 2ZPX ARG B   89  UNP  P01375    THR   165 ENGINEERED
SEQADV 2ZPX PRO B   90  UNP  P01375    LYS   166 ENGINEERED
SEQADV 2ZPX ARG B   98  UNP  P01375    LYS   174 ENGINEERED
SEQADV 2ZPX ASN B  112  UNP  P01375    LYS   188 ENGINEERED
SEQADV 2ZPX PRO B  128  UNP  P01375    LYS   204 ENGINEERED
SEQADV 2ZPX MET C   11  UNP  P01375    LYS    87 ENGINEERED
SEQADV 2ZPX SER C   65  UNP  P01375    LYS   141 ENGINEERED
SEQADV 2ZPX THR C   84  UNP  P01375    ALA   160 ENGINEERED
SEQADV 2ZPX PRO C   85  UNP  P01375    VAL   161 ENGINEERED
SEQADV 2ZPX ALA C   86  UNP  P01375    SER   162 ENGINEERED
SEQADV 2ZPX ILE C   87  UNP  P01375    TYR   163 ENGINEERED
SEQADV 2ZPX ASN C   88  UNP  P01375    GLN   164 ENGINEERED
SEQADV 2ZPX ARG C   89  UNP  P01375    THR   165 ENGINEERED
SEQADV 2ZPX PRO C   90  UNP  P01375    LYS   166 ENGINEERED
SEQADV 2ZPX ARG C   98  UNP  P01375    LYS   174 ENGINEERED
SEQADV 2ZPX ASN C  112  UNP  P01375    LYS   188 ENGINEERED
SEQADV 2ZPX PRO C  128  UNP  P01375    LYS   204 ENGINEERED
SEQRES   1 A  157  VAL ARG SER SER SER ARG THR PRO SER ASP MET 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 ARG 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 SER
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 THR PRO ALA ILE ASN ARG PRO VAL
SEQRES   8 A  157  ASN LEU LEU SER ALA ILE ARG SER PRO CYS GLN ARG GLU
SEQRES   9 A  157  THR PRO GLU GLY ALA GLU ALA ASN PRO TRP TYR GLU PRO
SEQRES  10 A  157  ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU PRO 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 B  157  VAL ARG SER SER SER ARG THR PRO SER ASP MET PRO VAL
SEQRES   2 B  157  ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU
SEQRES   3 B  157  GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN
SEQRES   4 B  157  GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER
SEQRES   5 B  157  GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SER
SEQRES   6 B  157  GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS
SEQRES   7 B  157  THR ILE SER ARG ILE THR PRO ALA ILE ASN ARG PRO VAL
SEQRES   8 B  157  ASN LEU LEU SER ALA ILE ARG SER PRO CYS GLN ARG GLU
SEQRES   9 B  157  THR PRO GLU GLY ALA GLU ALA ASN PRO TRP TYR GLU PRO
SEQRES  10 B  157  ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU PRO GLY ASP
SEQRES  11 B  157  ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU ASP
SEQRES  12 B  157  PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA
SEQRES  13 B  157  LEU
SEQRES   1 C  157  VAL ARG SER SER SER ARG THR PRO SER ASP MET 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 SER
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 THR PRO ALA ILE ASN ARG PRO VAL
SEQRES   8 C  157  ASN LEU LEU SER ALA ILE ARG SER PRO CYS GLN ARG GLU
SEQRES   9 C  157  THR PRO GLU GLY ALA GLU ALA ASN PRO TRP TYR GLU PRO
SEQRES  10 C  157  ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU PRO 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   *7(H2 O)
SHEET    1   A 5 LEU A  36  ALA A  38  0
SHEET    2   A 5 VAL A  13  VAL A  17 -1  N  VAL A  13   O  ALA A  38
SHEET    3   A 5 TYR A 151  ALA A 156 -1  O  ILE A 154   N  ALA A  14
SHEET    4   A 5 GLY A  54  GLN A  67 -1  N  TYR A  59   O  GLY A 153
SHEET    5   A 5 PRO A 113  LEU A 126 -1  O  LEU A 126   N  GLY A  54
SHEET    1   B 5 GLU A  42  LEU A  43  0
SHEET    2   B 5 LEU A  48  VAL A  49 -1  O  VAL A  49   N  GLU A  42
SHEET    3   B 5 ARG A 131  ILE A 136 -1  O  LEU A 132   N  LEU A  48
SHEET    4   B 5 LEU A  76  ILE A  83 -1  N  THR A  79   O  GLU A 135
SHEET    5   B 5 PRO A  90  ARG A  98 -1  O  ARG A  98   N  LEU A  76
SHEET    1   C 5 LEU B  36  ALA B  38  0
SHEET    2   C 5 VAL B  13  VAL B  17 -1  N  VAL B  13   O  ALA B  38
SHEET    3   C 5 TYR B 151  ALA B 156 -1  O  ILE B 154   N  ALA B  14
SHEET    4   C 5 GLY B  54  GLN B  67 -1  N  TYR B  59   O  GLY B 153
SHEET    5   C 5 PRO B 113  LEU B 126 -1  O  LEU B 126   N  GLY B  54
SHEET    1   D 5 GLU B  42  LEU B  43  0
SHEET    2   D 5 LEU B  48  VAL B  49 -1  O  VAL B  49   N  GLU B  42
SHEET    3   D 5 ARG B 131  ILE B 136 -1  O  LEU B 132   N  LEU B  48
SHEET    4   D 5 LEU B  76  SER B  81 -1  N  THR B  79   O  GLU B 135
SHEET    5   D 5 ASN B  92  ARG B  98 -1  O  ARG B  98   N  LEU B  76
SHEET    1   E 5 LEU C  36  ALA C  38  0
SHEET    2   E 5 VAL C  13  VAL C  17 -1  N  VAL C  13   O  ALA C  38
SHEET    3   E 5 TYR C 151  ALA C 156 -1  O  ILE C 154   N  ALA C  14
SHEET    4   E 5 GLY C  54  GLN C  67 -1  N  TYR C  59   O  GLY C 153
SHEET    5   E 5 PRO C 113  LEU C 126 -1  O  LEU C 126   N  GLY C  54
SHEET    1   F 5 LEU C  36  ALA C  38  0
SHEET    2   F 5 VAL C  13  VAL C  17 -1  N  VAL C  13   O  ALA C  38
SHEET    3   F 5 TYR C 151  ALA C 156 -1  O  ILE C 154   N  ALA C  14
SHEET    4   F 5 GLY C  54  GLN C  67 -1  N  TYR C  59   O  GLY C 153
SHEET    5   F 5 LEU C 142  ASP C 143 -1  O  ASP C 143   N  LEU C  63
SHEET    1   G 5 GLU C  42  LEU C  43  0
SHEET    2   G 5 LEU C  48  VAL C  49 -1  O  VAL C  49   N  GLU C  42
SHEET    3   G 5 ARG C 131  ILE C 136 -1  O  LEU C 132   N  LEU C  48
SHEET    4   G 5 LEU C  76  ILE C  83 -1  N  ILE C  83   O  ARG C 131
SHEET    5   G 5 VAL C  91  ARG C  98 -1  O  ARG C  98   N  LEU C  76
SSBOND   1 CYS A   69    CYS A  101                          1555   1555  2.03
SSBOND   2 CYS B   69    CYS B  101                          1555   1555  2.04
SSBOND   3 CYS C   69    CYS C  101                          1555   1555  2.03
CRYST1   49.586  111.331   75.382  90.00  90.00  90.00 P 21 21 21   12
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      0.020167  0.000000  0.000000        0.00000
SCALE2      0.000000  0.008982  0.000000        0.00000
SCALE3      0.000000  0.000000  0.013266        0.00000
      
PROCHECK
Go to PROCHECK summary
 References