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PDBsum entry 2zjc

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Cytokine PDB id
2zjc
Jmol
Contents
Protein chains
142 a.a.
151 a.a.
Ligands
GOL
Waters ×59
HEADER    CYTOKINE                                05-MAR-08   2ZJC
TITLE     TNFR1 SELECTVE TNF MUTANT; R1-6
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: TUMOR NECROSIS FACTOR;
COMPND   3 CHAIN: A, B, C;
COMPND   4 FRAGMENT: R1-6, UNP RESIDUES 77-233;
COMPND   5 SYNONYM: TNF-ALPHA, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER
COMPND   6 2, TNF-A, CACHECTIN;
COMPND   7 ENGINEERED: YES;
COMPND   8 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: TNF, TNFA, TNFSF2;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PYAS(MODIFED FROM PUC VECTOR)
KEYWDS    PHAGE DISPLAY SYSTEM, TNFR1 SELECTIVITY, TNF, AGONIST, MUTANT,
KEYWDS   2 CYTOKINE, LIPOPROTEIN, MEMBRANE, MYRISTATE, PHOSPHOPROTEIN,
KEYWDS   3 SECRETED, SIGNAL-ANCHOR, TRANSMEMBRANE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    Y.MUKAI,Y.YAMAGATA,Y.TSUTSUMI
REVDAT   3   13-JUL-11 2ZJC    1       VERSN
REVDAT   2   03-FEB-09 2ZJC    1       JRNL
REVDAT   1   20-JAN-09 2ZJC    0
JRNL        AUTH   Y.MUKAI,H.SHIBATA,T.NAKAMURA,Y.YOSHIOKA,Y.ABE,T.NOMURA,
JRNL        AUTH 2 M.TANIAI,T.OHTA,S.IKEMIZU,S.NAKAGAWA,S.TSUNODA,H.KAMADA,
JRNL        AUTH 3 Y.YAMAGATA,Y.TSUTSUMI
JRNL        TITL   STRUCTURE-FUNCTION RELATIONSHIP OF TUMOR NECROSIS FACTOR
JRNL        TITL 2 (TNF) AND ITS RECEPTOR INTERACTION BASED ON 3D STRUCTURAL
JRNL        TITL 3 ANALYSIS OF A FULLY ACTIVE TNFR1-SELECTIVE TNF MUTANT
JRNL        REF    J.MOL.BIOL.                   V. 385  1221 2009
JRNL        REFN                   ISSN 0022-2836
JRNL        PMID   19084540
JRNL        DOI    10.1016/J.JMB.2008.11.053
REMARK   2
REMARK   2 RESOLUTION.    2.50 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0019
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 25.67
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.1
REMARK   3   NUMBER OF REFLECTIONS             : 12060
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.209
REMARK   3   R VALUE            (WORKING SET) : 0.201
REMARK   3   FREE R VALUE                     : 0.272
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.200
REMARK   3   FREE R VALUE TEST SET COUNT      : 1373
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 20
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.50
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.56
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 798
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 84.23
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3180
REMARK   3   BIN FREE R VALUE SET COUNT          : 67
REMARK   3   BIN FREE R VALUE                    : 0.4060
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3338
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 6
REMARK   3   SOLVENT ATOMS            : 59
REMARK   3
REMARK   3  B VALUES.
REMARK   3   B VALUE TYPE : LIKELY RESIDUAL
REMARK   3   FROM WILSON PLOT           (A**2) : 19.60
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 19.70
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 1.17000
REMARK   3    B22 (A**2) : 1.17000
REMARK   3    B33 (A**2) : -1.76000
REMARK   3    B12 (A**2) : 0.59000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): NULL
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.378
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.329
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.501
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.945
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.900
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  3429 ; 0.009 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  4696 ; 1.271 ; 1.964
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   430 ; 6.788 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   154 ;38.485 ;24.805
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   500 ;19.605 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    16 ;21.308 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   530 ; 0.089 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2666 ; 0.004 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1488 ; 0.201 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2260 ; 0.309 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   141 ; 0.157 ; 0.200
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    63 ; 0.199 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):     8 ; 0.191 ; 0.200
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  2219 ; 0.425 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3506 ; 0.766 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1374 ; 0.938 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1190 ; 1.483 ; 4.500
REMARK   3
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  NCS RESTRAINTS STATISTICS
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : 3
REMARK   3
REMARK   3   TLS GROUP : 1
REMARK   3    NUMBER OF COMPONENTS GROUP : 1
REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI
REMARK   3    RESIDUE RANGE :   A     8        A   157
REMARK   3    ORIGIN FOR THE GROUP (A):   0.5060  19.7770  -2.4510
REMARK   3    T TENSOR
REMARK   3      T11:  -0.0303 T22:  -0.1278
REMARK   3      T33:   0.6965 T12:  -0.0072
REMARK   3      T13:   0.0522 T23:  -0.0744
REMARK   3    L TENSOR
REMARK   3      L11:   7.2741 L22:   5.0031
REMARK   3      L33:   2.1215 L12:  -0.7318
REMARK   3      L13:   0.4993 L23:  -0.2757
REMARK   3    S TENSOR
REMARK   3      S11:   0.1049 S12:   0.4883 S13:  -0.7046
REMARK   3      S21:  -0.4488 S22:   0.0210 S23:  -0.1429
REMARK   3      S31:   0.0590 S32:   0.0964 S33:  -0.1259
REMARK   3
REMARK   3   TLS GROUP : 2
REMARK   3    NUMBER OF COMPONENTS GROUP : 1
REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI
REMARK   3    RESIDUE RANGE :   B     6        B   157
REMARK   3    ORIGIN FOR THE GROUP (A):  -8.0410  22.0520  17.3240
REMARK   3    T TENSOR
REMARK   3      T11:  -0.0391 T22:   0.0557
REMARK   3      T33:   0.6702 T12:   0.0665
REMARK   3      T13:   0.0867 T23:   0.1508
REMARK   3    L TENSOR
REMARK   3      L11:   8.4563 L22:   2.5695
REMARK   3      L33:   2.5998 L12:   0.3446
REMARK   3      L13:   2.6144 L23:   0.3406
REMARK   3    S TENSOR
REMARK   3      S11:  -0.0378 S12:  -0.6922 S13:  -0.7246
REMARK   3      S21:   0.2925 S22:   0.0528 S23:  -0.1898
REMARK   3      S31:   0.1934 S32:  -0.0944 S33:  -0.0150
REMARK   3
REMARK   3   TLS GROUP : 3
REMARK   3    NUMBER OF COMPONENTS GROUP : 1
REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI
REMARK   3    RESIDUE RANGE :   C     8        C   157
REMARK   3    ORIGIN FOR THE GROUP (A):  -3.9240  39.8210   5.1670
REMARK   3    T TENSOR
REMARK   3      T11:  -0.0377 T22:  -0.0837
REMARK   3      T33:   0.6419 T12:   0.0347
REMARK   3      T13:  -0.0158 T23:  -0.0348
REMARK   3    L TENSOR
REMARK   3      L11:   4.6971 L22:   2.8298
REMARK   3      L33:   2.2781 L12:   0.0598
REMARK   3      L13:   0.0282 L23:  -0.4122
REMARK   3    S TENSOR
REMARK   3      S11:  -0.0870 S12:  -0.1554 S13:   0.3628
REMARK   3      S21:   0.0194 S22:   0.0632 S23:  -0.1324
REMARK   3      S31:  -0.1994 S32:  -0.0371 S33:   0.0238
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK   3  POSITIONS
REMARK   4
REMARK   4 2ZJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-08.
REMARK 100 THE RCSB ID CODE IS RCSB028044.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 13-DEC-03
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          : ADSC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 13445
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.500
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.9
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : 0.10300
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 28.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.59
REMARK 200  COMPLETENESS FOR SHELL     (%) : 85.2
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : 0.53000
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 4.200
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   (%): 38.85
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP,
REMARK 280  TEMPERATURE 293K, PH6.5
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       67.93650
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       39.22316
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       19.34100
REMARK 290   SMTRY1   5 -0.500000 -0.866025  0.000000       67.93650
REMARK 290   SMTRY2   5  0.866025 -0.500000  0.000000       39.22316
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       19.34100
REMARK 290   SMTRY1   6 -0.500000  0.866025  0.000000       67.93650
REMARK 290   SMTRY2   6 -0.866025 -0.500000  0.000000       39.22316
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       19.34100
REMARK 290   SMTRY1   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       78.44631
REMARK 290   SMTRY3   7  0.000000  0.000000  1.000000       38.68200
REMARK 290   SMTRY1   8 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   8  0.866025 -0.500000  0.000000       78.44631
REMARK 290   SMTRY3   8  0.000000  0.000000  1.000000       38.68200
REMARK 290   SMTRY1   9 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   9 -0.866025 -0.500000  0.000000       78.44631
REMARK 290   SMTRY3   9  0.000000  0.000000  1.000000       38.68200
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: 7180 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17010 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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     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: 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       68.73    -66.59
REMARK 500    THR A  89      105.84   -161.77
REMARK 500    GLN B  21      -38.37   -140.15
REMARK 500    GLU B  23      -40.34    -23.42
REMARK 500    GLU B 110      122.27    -39.01
REMARK 500    PHE B 144     -147.70     55.61
REMARK 500    THR B 147      140.06    -39.72
REMARK 500    SER C   9     -151.14   -135.11
REMARK 500    LEU C  37       87.39   -179.33
REMARK 500    ASP C  45       46.69     35.74
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    CYS C 101        23.1      L          L   OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 158
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2E7A   RELATED DB: PDB
REMARK 900 TNF RECEPTOR SUBTYPE ONE-SELECTIVE TNF MUTANT WITH
REMARK 900 ANTAGONISTIC ACTIVITY
DBREF  2ZJC A    1   157  UNP    P01375   TNFA_HUMAN      77    233
DBREF  2ZJC B    1   157  UNP    P01375   TNFA_HUMAN      77    233
DBREF  2ZJC C    1   157  UNP    P01375   TNFA_HUMAN      77    233
SEQADV 2ZJC MET A   11  UNP  P01375    LYS    87 ENGINEERED
SEQADV 2ZJC LYS A   29  UNP  P01375    LEU   105 ENGINEERED
SEQADV 2ZJC ALA A   31  UNP  P01375    ARG   107 ENGINEERED
SEQADV 2ZJC GLY A   32  UNP  P01375    ARG   108 ENGINEERED
SEQADV 2ZJC SER A   65  UNP  P01375    LYS   141 ENGINEERED
SEQADV 2ZJC PRO A   90  UNP  P01375    LYS   166 ENGINEERED
SEQADV 2ZJC ARG A   98  UNP  P01375    LYS   174 ENGINEERED
SEQADV 2ZJC ASN A  112  UNP  P01375    LYS   188 ENGINEERED
SEQADV 2ZJC PRO A  128  UNP  P01375    LYS   204 ENGINEERED
SEQADV 2ZJC SER A  146  UNP  P01375    GLU   222 ENGINEERED
SEQADV 2ZJC THR A  147  UNP  P01375    SER   223 ENGINEERED
SEQADV 2ZJC MET B   11  UNP  P01375    LYS    87 ENGINEERED
SEQADV 2ZJC LYS B   29  UNP  P01375    LEU   105 ENGINEERED
SEQADV 2ZJC ALA B   31  UNP  P01375    ARG   107 ENGINEERED
SEQADV 2ZJC GLY B   32  UNP  P01375    ARG   108 ENGINEERED
SEQADV 2ZJC SER B   65  UNP  P01375    LYS   141 ENGINEERED
SEQADV 2ZJC PRO B   90  UNP  P01375    LYS   166 ENGINEERED
SEQADV 2ZJC ARG B   98  UNP  P01375    LYS   174 ENGINEERED
SEQADV 2ZJC ASN B  112  UNP  P01375    LYS   188 ENGINEERED
SEQADV 2ZJC PRO B  128  UNP  P01375    LYS   204 ENGINEERED
SEQADV 2ZJC SER B  146  UNP  P01375    GLU   222 ENGINEERED
SEQADV 2ZJC THR B  147  UNP  P01375    SER   223 ENGINEERED
SEQADV 2ZJC MET C   11  UNP  P01375    LYS    87 ENGINEERED
SEQADV 2ZJC LYS C   29  UNP  P01375    LEU   105 ENGINEERED
SEQADV 2ZJC ALA C   31  UNP  P01375    ARG   107 ENGINEERED
SEQADV 2ZJC GLY C   32  UNP  P01375    ARG   108 ENGINEERED
SEQADV 2ZJC SER C   65  UNP  P01375    LYS   141 ENGINEERED
SEQADV 2ZJC PRO C   90  UNP  P01375    LYS   166 ENGINEERED
SEQADV 2ZJC ARG C   98  UNP  P01375    LYS   174 ENGINEERED
SEQADV 2ZJC ASN C  112  UNP  P01375    LYS   188 ENGINEERED
SEQADV 2ZJC PRO C  128  UNP  P01375    LYS   204 ENGINEERED
SEQADV 2ZJC SER C  146  UNP  P01375    GLU   222 ENGINEERED
SEQADV 2ZJC THR C  147  UNP  P01375    SER   223 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 LYS ASN ALA GLY 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 ALA VAL SER TYR GLN THR 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 SER THR 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 LYS ASN ALA GLY 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 ALA VAL SER TYR GLN THR 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 SER THR 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 LYS ASN ALA GLY 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 ALA VAL SER TYR GLN THR 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 SER THR GLY GLN VAL TYR PHE GLY ILE ILE ALA
SEQRES  13 C  157  LEU
HET    GOL  B 158       6
HETNAM     GOL GLYCEROL
HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL   4  GOL    C3 H8 O3
FORMUL   5  HOH   *59(H2 O)
HELIX    1   1 ARG A  138  LEU A  142  5                                   5
HELIX    2   2 ARG C  138  LEU C  142  5                                   5
SHEET    1   A 3 TRP A  28  LYS A  29  0
SHEET    2   A 3 VAL A  13  ALA A  18 -1  N  VAL A  17   O  LYS 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  LYS A  29  0
SHEET    2   B 5 VAL A  13  ALA A  18 -1  N  VAL A  17   O  LYS 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  GLY A  66 -1  N  LEU A  55   O  LEU A 157
SHEET    5   B 5 TRP A 114  LEU A 126 -1  O  LEU A 120   N  SER A  60
SHEET    1   C 5 GLU A  42  ARG A  44  0
SHEET    2   C 5 GLN A  47  VAL A  49 -1  O  GLN A  47   N  ARG A  44
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 VAL A  91  ARG A  98 -1  O  LEU A  93   N  ILE A  80
SHEET    1   D 3 GLN B  27  LYS B  29  0
SHEET    2   D 3 VAL B  13  ASN B  19 -1  N  VAL B  17   O  LYS B  29
SHEET    3   D 3 LEU B  36  ALA B  38 -1  O  LEU B  36   N  HIS B  15
SHEET    1   E 5 GLN B  27  LYS B  29  0
SHEET    2   E 5 VAL B  13  ASN B  19 -1  N  VAL B  17   O  LYS B  29
SHEET    3   E 5 TYR B 151  LEU B 157 -1  O  PHE B 152   N  VAL B  16
SHEET    4   E 5 GLY B  54  GLN B  67 -1  N  LEU B  55   O  LEU B 157
SHEET    5   E 5 PRO B 113  LEU B 126 -1  O  GLY B 122   N  ILE B  58
SHEET    1   F 5 GLU B  42  ARG B  44  0
SHEET    2   F 5 GLN B  47  VAL B  49 -1  O  VAL B  49   N  GLU B  42
SHEET    3   F 5 ARG B 131  ILE B 136 -1  O  LEU B 132   N  LEU B  48
SHEET    4   F 5 LEU B  76  ILE B  83 -1  N  ILE B  83   O  ARG B 131
SHEET    5   F 5 VAL B  91  ARG B  98 -1  O  ARG B  98   N  LEU B  76
SHEET    1   G 3 TRP C  28  LYS C  29  0
SHEET    2   G 3 VAL C  13  ALA C  18 -1  N  VAL C  17   O  LYS C  29
SHEET    3   G 3 LEU C  36  ALA C  38 -1  O  ALA C  38   N  VAL C  13
SHEET    1   H 5 TRP C  28  LYS C  29  0
SHEET    2   H 5 VAL C  13  ALA C  18 -1  N  VAL C  17   O  LYS C  29
SHEET    3   H 5 TYR C 151  ALA C 156 -1  O  PHE C 152   N  VAL C  16
SHEET    4   H 5 GLY C  54  GLY C  66 -1  N  GLN C  61   O  TYR C 151
SHEET    5   H 5 TRP C 114  LEU C 126 -1  O  PHE C 124   N  TYR C  56
SHEET    1   I 5 GLU C  42  ARG C  44  0
SHEET    2   I 5 GLN C  47  VAL C  49 -1  O  GLN C  47   N  ARG C  44
SHEET    3   I 5 ARG C 131  ILE C 136 -1  O  LEU C 132   N  LEU C  48
SHEET    4   I 5 LEU C  76  ILE C  83 -1  N  THR C  79   O  GLU C 135
SHEET    5   I 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  2.04
SSBOND   2 CYS B   69    CYS B  101                          1555   1555  2.03
SSBOND   3 CYS C   69    CYS C  101                          1555   1555  2.01
CISPEP   1 PHE B  144    ALA B  145          0       -29.33
SITE     1 AC1  7 PRO A 117  ILE A 118  TYR A 119  ARG B  98
SITE     2 AC1  7 ILE B 118  TYR B 119  ARG C  98
CRYST1  135.873  135.873   58.023  90.00  90.00 120.00 H 3          27
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      0.007360  0.004249  0.000000        0.00000
SCALE2      0.000000  0.008498  0.000000        0.00000
SCALE3      0.000000  0.000000  0.017235        0.00000
      
PROCHECK
Go to PROCHECK summary
 References