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PDBsum entry 2az5

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Top Page protein ligands Protein-protein interface(s) links
Cytokine PDB id
2az5
Jmol
Contents
Protein chains
132 a.a.
140 a.a.
Ligands
307 ×2
Waters ×226
HEADER    CYTOKINE                                09-SEP-05   2AZ5
TITLE     CRYSTAL STRUCTURE OF TNF-ALPHA WITH A SMALL MOLECULE
TITLE    2 INHIBITOR
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: TUMOR NECROSIS FACTOR (TNF-ALPHA) (TUMOR
COMPND   3 NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 2) (TNF-A)
COMPND   4 (CACHECTIN) [CONTAINS: TUMOR NECROSIS FACTOR, MEMBRANE
COMPND   5 FORM; TUMOR NECROSIS FACTOR, SOLUBLE FORM];
COMPND   6 CHAIN: A, B, C, D;
COMPND   7 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: TNF, TNFA, TNFSF2;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PRSET
KEYWDS    TNF-ALPHA TRIMER DISRUPTION BY BINDING OF A SMALL MOLECULE
KEYWDS   2 INHIBITOR, CYTOKINE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.M.HE
REVDAT   4   24-FEB-09 2AZ5    1       VERSN
REVDAT   3   18-APR-06 2AZ5    1       AUTHOR
REVDAT   2   06-DEC-05 2AZ5    1       AUTHOR
REVDAT   1   29-NOV-05 2AZ5    0
JRNL        AUTH   M.M.HE,A.S.SMITH,J.D.OSLOB,W.M.FLANAGAN,
JRNL        AUTH 2 A.C.BRAISTED,A.WHITTY,M.T.CANCILLA,J.WANG,
JRNL        AUTH 3 A.A.LUGOVSKOY,J.C.YOBURN,A.D.FUNG,G.FARRINGTON,
JRNL        AUTH 4 J.K.ELDREDGE,E.S.DAY,L.A.CRUZ,T.G.CACHERO,
JRNL        AUTH 5 S.K.MILLER,J.E.FRIEDMAN,I.C.CHOONG,B.C.CUNNINGHAM
JRNL        TITL   SMALL-MOLECULE INHIBITION OF TNF-ALPHA.
JRNL        REF    SCIENCE                       V. 310  1022 2005
JRNL        REFN                   ISSN 0036-8075
JRNL        PMID   16284179
JRNL        DOI    10.1126/SCIENCE.1116304
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    2.10 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0005
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) : 2.10
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.2
REMARK   3   NUMBER OF REFLECTIONS             : 37535
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) : 0.227
REMARK   3   R VALUE            (WORKING SET) : 0.220
REMARK   3   FREE R VALUE                     : 0.278
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 1916
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 15
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.10
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.17
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 3496
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 99.95
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2270
REMARK   3   BIN FREE R VALUE SET COUNT          : 196
REMARK   3   BIN FREE R VALUE                    : 0.2830
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 4194
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 80
REMARK   3   SOLVENT ATOMS            : 226
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 36.78
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.57000
REMARK   3    B22 (A**2) : -0.57000
REMARK   3    B33 (A**2) : 0.86000
REMARK   3    B12 (A**2) : -0.29000
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): 0.231
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.212
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.153
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.550
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.940
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.891
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  4376 ; 0.007 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  5968 ; 1.396 ; 1.989
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   531 ; 6.734 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   184 ;39.195 ;24.511
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   684 ;14.902 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    20 ;15.132 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   672 ; 0.091 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  3302 ; 0.006 ; 0.020
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1854 ; 0.203 ; 0.200
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2908 ; 0.311 ; 0.200
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   278 ; 0.139 ; 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):    70 ; 0.185 ; 0.200
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    12 ; 0.072 ; 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):  2757 ; 3.420 ; 2.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  4319 ; 4.870 ; 5.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1976 ; 3.598 ; 2.500
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1649 ; 5.359 ; 5.000
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  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : BABINET MODEL WITH 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: NULL
REMARK   4
REMARK   4 2AZ5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-05.
REMARK 100 THE RCSB ID CODE IS RCSB034476.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 14-MAR-03
REMARK 200  TEMPERATURE           (KELVIN) : NULL
REMARK 200  PH                             : 7.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : SSRL
REMARK 200  BEAMLINE                       : BL7-1
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.0
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : CCP4 (SCALA)
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 37559
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.100
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL
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: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY: 1TNF
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 48.30
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M SODIUM FORMATE, PH 7.5, VAPOR
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 323K
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       82.62700
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       47.70472
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       21.24267
REMARK 290   SMTRY1   5 -0.500000 -0.866025  0.000000       82.62700
REMARK 290   SMTRY2   5  0.866025 -0.500000  0.000000       47.70472
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       21.24267
REMARK 290   SMTRY1   6 -0.500000  0.866025  0.000000       82.62700
REMARK 290   SMTRY2   6 -0.866025 -0.500000  0.000000       47.70472
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       21.24267
REMARK 290   SMTRY1   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       95.40944
REMARK 290   SMTRY3   7  0.000000  0.000000  1.000000       42.48533
REMARK 290   SMTRY1   8 -0.500000 -0.866025  0.000000        0.00000
REMARK 290   SMTRY2   8  0.866025 -0.500000  0.000000       95.40944
REMARK 290   SMTRY3   8  0.000000  0.000000  1.000000       42.48533
REMARK 290   SMTRY1   9 -0.500000  0.866025  0.000000        0.00000
REMARK 290   SMTRY2   9 -0.866025 -0.500000  0.000000       95.40944
REMARK 290   SMTRY3   9  0.000000  0.000000  1.000000       42.48533
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D
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     ARG A    31
REMARK 465     ARG A    32
REMARK 465     ALA A    33
REMARK 465     ASN A    34
REMARK 465     ALA A    35
REMARK 465     GLN A   102
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     ALA A   111
REMARK 465     LYS A   112
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     ALA B   111
REMARK 465     ARG C    31
REMARK 465     ARG C    32
REMARK 465     ALA C    33
REMARK 465     ASN C    34
REMARK 465     ALA C    35
REMARK 465     SER C    86
REMARK 465     TYR C    87
REMARK 465     GLN C    88
REMARK 465     GLN C   102
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 465     ALA C   111
REMARK 465     LYS C   112
REMARK 465     GLU D   104
REMARK 465     THR D   105
REMARK 465     PRO D   106
REMARK 465     GLU D   107
REMARK 465     GLY D   108
REMARK 465     ALA D   109
REMARK 465     GLU D   110
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     ASP A  10    CG   OD1  OD2
REMARK 470     TYR A  87    CG   CD1  CD2  CE1  CE2  CZ   OH
REMARK 470     GLU A 146    CG   CD   OE1  OE2
REMARK 470     LEU A 157    O
REMARK 470     ASP B  10    CG   OD1  OD2
REMARK 470     GLU B  23    CG   CD   OE1  OE2
REMARK 470     ARG B 103    CG   CD   NE   CZ   NH1  NH2
REMARK 470     GLU B 146    CG   CD   OE1  OE2
REMARK 470     LEU B 157    O
REMARK 470     ASP C  10    CG   OD1  OD2
REMARK 470     LEU C 157    O
REMARK 470     ASP D  10    CG   OD1  OD2
REMARK 470     GLU D  23    CG   CD   OE1  OE2
REMARK 470     TYR D  87    CG   CD1  CD2  CE1  CE2  CZ   OH
REMARK 470     ARG D 103    CG   CD   NE   CZ   NH1  NH2
REMARK 470     LYS D 112    CG   CD   CE   NZ
REMARK 470     LEU D 157    O
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    LEU A  37       84.55   -151.55
REMARK 500    PRO A  70     -163.08    -79.33
REMARK 500    ARG B  31       43.78    -86.43
REMARK 500    GLN B  88       -9.14     60.17
REMARK 500    LEU C  37       84.47   -156.29
REMARK 500    PRO C  70     -153.34    -78.81
REMARK 500    ARG D  31       49.70    -83.03
REMARK 500    GLN D  88        5.58    -58.85
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 307 A 1
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 307 C 2
DBREF  2AZ5 A   10   157  UNP    P01375   TNFA_HUMAN      86    233
DBREF  2AZ5 B   10   157  UNP    P01375   TNFA_HUMAN      86    233
DBREF  2AZ5 C   10   157  UNP    P01375   TNFA_HUMAN      86    233
DBREF  2AZ5 D   10   157  UNP    P01375   TNFA_HUMAN      86    233
SEQRES   1 A  148  ASP LYS PRO VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA
SEQRES   2 A  148  GLU GLY GLN LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA
SEQRES   3 A  148  LEU LEU ALA ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU
SEQRES   4 A  148  VAL VAL PRO SER GLU GLY LEU TYR LEU ILE TYR SER GLN
SEQRES   5 A  148  VAL LEU PHE LYS GLY GLN GLY CYS PRO SER THR HIS VAL
SEQRES   6 A  148  LEU LEU THR HIS THR ILE SER ARG ILE ALA VAL SER TYR
SEQRES   7 A  148  GLN THR LYS VAL ASN LEU LEU SER ALA ILE LYS SER PRO
SEQRES   8 A  148  CYS GLN ARG GLU THR PRO GLU GLY ALA GLU ALA LYS PRO
SEQRES   9 A  148  TRP TYR GLU PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU
SEQRES  10 A  148  GLU LYS GLY ASP ARG LEU SER ALA GLU ILE ASN ARG PRO
SEQRES  11 A  148  ASP TYR LEU ASP PHE ALA GLU SER GLY GLN VAL TYR PHE
SEQRES  12 A  148  GLY ILE ILE ALA LEU
SEQRES   1 B  148  ASP LYS PRO VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA
SEQRES   2 B  148  GLU GLY GLN LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA
SEQRES   3 B  148  LEU LEU ALA ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU
SEQRES   4 B  148  VAL VAL PRO SER GLU GLY LEU TYR LEU ILE TYR SER GLN
SEQRES   5 B  148  VAL LEU PHE LYS GLY GLN GLY CYS PRO SER THR HIS VAL
SEQRES   6 B  148  LEU LEU THR HIS THR ILE SER ARG ILE ALA VAL SER TYR
SEQRES   7 B  148  GLN THR LYS VAL ASN LEU LEU SER ALA ILE LYS SER PRO
SEQRES   8 B  148  CYS GLN ARG GLU THR PRO GLU GLY ALA GLU ALA LYS PRO
SEQRES   9 B  148  TRP TYR GLU PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU
SEQRES  10 B  148  GLU LYS GLY ASP ARG LEU SER ALA GLU ILE ASN ARG PRO
SEQRES  11 B  148  ASP TYR LEU ASP PHE ALA GLU SER GLY GLN VAL TYR PHE
SEQRES  12 B  148  GLY ILE ILE ALA LEU
SEQRES   1 C  148  ASP LYS PRO VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA
SEQRES   2 C  148  GLU GLY GLN LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA
SEQRES   3 C  148  LEU LEU ALA ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU
SEQRES   4 C  148  VAL VAL PRO SER GLU GLY LEU TYR LEU ILE TYR SER GLN
SEQRES   5 C  148  VAL LEU PHE LYS GLY GLN GLY CYS PRO SER THR HIS VAL
SEQRES   6 C  148  LEU LEU THR HIS THR ILE SER ARG ILE ALA VAL SER TYR
SEQRES   7 C  148  GLN THR LYS VAL ASN LEU LEU SER ALA ILE LYS SER PRO
SEQRES   8 C  148  CYS GLN ARG GLU THR PRO GLU GLY ALA GLU ALA LYS PRO
SEQRES   9 C  148  TRP TYR GLU PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU
SEQRES  10 C  148  GLU LYS GLY ASP ARG LEU SER ALA GLU ILE ASN ARG PRO
SEQRES  11 C  148  ASP TYR LEU ASP PHE ALA GLU SER GLY GLN VAL TYR PHE
SEQRES  12 C  148  GLY ILE ILE ALA LEU
SEQRES   1 D  148  ASP LYS PRO VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA
SEQRES   2 D  148  GLU GLY GLN LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA
SEQRES   3 D  148  LEU LEU ALA ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU
SEQRES   4 D  148  VAL VAL PRO SER GLU GLY LEU TYR LEU ILE TYR SER GLN
SEQRES   5 D  148  VAL LEU PHE LYS GLY GLN GLY CYS PRO SER THR HIS VAL
SEQRES   6 D  148  LEU LEU THR HIS THR ILE SER ARG ILE ALA VAL SER TYR
SEQRES   7 D  148  GLN THR LYS VAL ASN LEU LEU SER ALA ILE LYS SER PRO
SEQRES   8 D  148  CYS GLN ARG GLU THR PRO GLU GLY ALA GLU ALA LYS PRO
SEQRES   9 D  148  TRP TYR GLU PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU
SEQRES  10 D  148  GLU LYS GLY ASP ARG LEU SER ALA GLU ILE ASN ARG PRO
SEQRES  11 D  148  ASP TYR LEU ASP PHE ALA GLU SER GLY GLN VAL TYR PHE
SEQRES  12 D  148  GLY ILE ILE ALA LEU
HET    307  A   1      40
HET    307  C   2      40
HETNAM     307 6,7-DIMETHYL-3-[(METHYL{2-[METHYL({1-[3-
HETNAM   2 307  (TRIFLUOROMETHYL)PHENYL]-1H-INDOL-3-YL}METHYL)
HETNAM   3 307  AMINO]ETHYL}AMINO)METHYL]-4H-CHROMEN-4-ONE
FORMUL   5  307    2(C32 H32 F3 N3 O2)
FORMUL   7  HOH   *226(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 ARG B  138  LEU B  142  5                                   5
HELIX    4   4 ARG C  138  LEU C  142  5                                   5
HELIX    5   5 ARG D  138  LEU D  142  5                                   5
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  37  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  ALA A 156 -1  O  PHE A 152   N  VAL A  16
SHEET    4   B 5 GLY A  54  GLY A  66 -1  N  TYR A  59   O  GLY A 153
SHEET    5   B 5 TRP A 114  LEU A 126 -1  O  PHE A 124   N  TYR A  56
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  LYS A  98   N  LEU A  76
SHEET    1   D 3 TRP B  28  LEU B  29  0
SHEET    2   D 3 VAL B  13  ALA B  18 -1  N  VAL B  17   O  LEU 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 TRP B  28  LEU B  29  0
SHEET    2   E 5 VAL B  13  ALA B  18 -1  N  VAL B  17   O  LEU B  29
SHEET    3   E 5 TYR B 151  ALA B 156 -1  O  PHE B 152   N  VAL B  16
SHEET    4   E 5 GLY B  54  GLN B  67 -1  N  TYR B  59   O  GLY B 153
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 LYS B  90  LYS B  98 -1  O  LEU B  93   N  ILE B  80
SHEET    1   G 3 TRP C  28  LEU C  29  0
SHEET    2   G 3 VAL C  13  ALA C  18 -1  N  VAL C  17   O  LEU C  29
SHEET    3   G 3 LEU C  37  ALA C  38 -1  O  ALA C  38   N  VAL C  13
SHEET    1   H 5 TRP C  28  LEU C  29  0
SHEET    2   H 5 VAL C  13  ALA C  18 -1  N  VAL C  17   O  LEU 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  TYR C  59   O  GLY C 153
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  VAL C  49   N  GLU C  42
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  ILE C  83   O  ARG C 131
SHEET    5   I 5 LYS C  90  LYS C  98 -1  O  LEU C  94   N  ILE C  80
SHEET    1   J 3 TRP D  28  LEU D  29  0
SHEET    2   J 3 VAL D  13  ALA D  18 -1  N  VAL D  17   O  LEU D  29
SHEET    3   J 3 LEU D  36  ALA D  38 -1  O  LEU D  36   N  HIS D  15
SHEET    1   K 5 TRP D  28  LEU D  29  0
SHEET    2   K 5 VAL D  13  ALA D  18 -1  N  VAL D  17   O  LEU D  29
SHEET    3   K 5 TYR D 151  ALA D 156 -1  O  PHE D 152   N  VAL D  16
SHEET    4   K 5 GLY D  54  GLN D  67 -1  N  TYR D  59   O  GLY D 153
SHEET    5   K 5 PRO D 113  LEU D 126 -1  O  LEU D 126   N  GLY D  54
SHEET    1   L 5 GLU D  42  ARG D  44  0
SHEET    2   L 5 GLN D  47  VAL D  49 -1  O  VAL D  49   N  GLU D  42
SHEET    3   L 5 ARG D 131  ILE D 136 -1  O  LEU D 132   N  LEU D  48
SHEET    4   L 5 LEU D  76  ALA D  84 -1  N  THR D  79   O  GLU D 135
SHEET    5   L 5 TYR D  87  LYS D  98 -1  O  LYS D  98   N  LEU D  76
SSBOND   1 CYS A   69    CYS A  101                          1555   1555  2.04
SSBOND   2 CYS B   69    CYS B  101                          1555   1555  2.06
SSBOND   3 CYS C   69    CYS C  101                          1555   1555  2.04
SSBOND   4 CYS D   69    CYS D  101                          1555   1555  2.06
SITE     1 AC1 12 LEU A  57  SER A  60  TYR A 119  LEU A 120
SITE     2 AC1 12 GLY A 121  GLY A 122  TYR A 151  TYR B  59
SITE     3 AC1 12 TYR B 119  LEU B 120  GLY B 121  TYR B 151
SITE     1 AC2 12 LEU C  57  SER C  60  TYR C 119  LEU C 120
SITE     2 AC2 12 GLY C 121  GLY C 122  TYR C 151  TYR D  59
SITE     3 AC2 12 SER D  60  TYR D 119  LEU D 120  GLY D 121
CRYST1  165.254  165.254   63.728  90.00  90.00 120.00 H 3          36
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      0.006050  0.003490  0.000000        0.00000
SCALE2      0.000000  0.006990  0.000000        0.00000
SCALE3      0.000000  0.000000  0.015690        0.00000
      
PROCHECK
Go to PROCHECK summary
 References