HEADER CYTOKINE 23-APR-19 6OOZ
TITLE ASYMMETRIC HTNF-ALPHA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR;
COMPND 3 CHAIN: A, B, C;
COMPND 4 SYNONYM: CACHECTIN,TNF-ALPHA,TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY
COMPND 5 MEMBER 2,TNF-A;
COMPND 6 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;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS TUMOUR NECROSIS FACTOR ALPHA, TNF, ASYMMETRIC, PROTEIN-PROTEIN
KEYWDS 2 INTERACTION INHIBITOR, RHEUMATOID ARTHRITIS, CYTOKINE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.L.ARAKAKI,T.E.EDWARDS,D.FOX III,F.LECOMTE,T.CESKA
REVDAT 4 30-OCT-24 6OOZ 1 REMARK
REVDAT 3 03-APR-24 6OOZ 1 REMARK
REVDAT 2 01-JAN-20 6OOZ 1 JRNL
REVDAT 1 25-DEC-19 6OOZ 0
JRNL AUTH J.O'CONNELL,J.PORTER,B.KROEPLIEN,T.NORMAN,S.RAPECKI,R.DAVIS,
JRNL AUTH 2 D.MCMILLAN,T.ARAKAKI,A.BURGIN,D.FOX III,T.CESKA,F.LECOMTE,
JRNL AUTH 3 A.MALONEY,A.VUGLER,B.CARRINGTON,B.P.COSSINS,T.BOURNE,
JRNL AUTH 4 A.LAWSON
JRNL TITL SMALL MOLECULES THAT INHIBIT TNF SIGNALLING BY STABILISING
JRNL TITL 2 AN ASYMMETRIC FORM OF THE TRIMER.
JRNL REF NAT COMMUN V. 10 5795 2019
JRNL REFN ESSN 2041-1723
JRNL PMID 31857588
JRNL DOI 10.1038/S41467-019-13616-1
REMARK 2
REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0158
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 10432
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) : 0.192
REMARK 3 R VALUE (WORKING SET) : 0.183
REMARK 3 FREE R VALUE : 0.273
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1028
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) : 2.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87
REMARK 3 REFLECTION IN BIN (WORKING SET) : 652
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.73
REMARK 3 BIN R VALUE (WORKING SET) : 0.2540
REMARK 3 BIN FREE R VALUE SET COUNT : 76
REMARK 3 BIN FREE R VALUE : 0.4070
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3162
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 27
REMARK 3 SOLVENT ATOMS : 44
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 38.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.23
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.69000
REMARK 3 B22 (A**2) : -1.66000
REMARK 3 B33 (A**2) : 0.97000
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 OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.465
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.330
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.861
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.864
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3258 ; 0.010 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 2993 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4440 ; 1.534 ; 1.971
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6900 ; 0.973 ; 2.993
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 403 ; 7.658 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;37.601 ;24.338
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 486 ;15.393 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;15.906 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 512 ; 0.110 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3610 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 640 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
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): 1648 ; 2.226 ; 3.903
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1647 ; 2.219 ; 3.902
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2039 ; 3.749 ; 5.819
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
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 : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED
REMARK 4
REMARK 4 6OOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-19.
REMARK 100 THE DEPOSITION ID IS D_1000241082.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 24-SEP-10
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 8.00
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALS
REMARK 200 BEAMLINE : 5.0.3
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9765
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10469
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 4.300
REMARK 200 R MERGE (I) : 0.09200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000
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) : 2.87
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7
REMARK 200 DATA REDUNDANCY IN SHELL : 4.40
REMARK 200 R MERGE FOR SHELL (I) : 0.52700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: UNPUBLISHED STRUCTURE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 36.90
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 2000, 15% PEG 3350, 3%
REMARK 280 XYLITOL, 0.1 M HEPES, PH 8.0, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 289K, PH 8.00
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 26.76000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.67500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.58500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.67500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.76000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.58500
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: 5080 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 18300 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 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 SER B 71
REMARK 465 THR B 72
REMARK 465 GLN B 102
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 VAL C 1
REMARK 465 ARG C 2
REMARK 465 SER C 3
REMARK 465 SER C 4
REMARK 465 SER C 5
REMARK 465 ARG C 6
REMARK 465 THR C 7
REMARK 465 PRO C 8
REMARK 465 SER C 9
REMARK 465 GLN C 21
REMARK 465 ALA C 22
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 LEU C 36
REMARK 465 LEU C 37
REMARK 465 PRO C 70
REMARK 465 SER C 71
REMARK 465 SER C 86
REMARK 465 TYR C 87
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 145
REMARK 465 GLU C 146
REMARK 465 SER C 147
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 LYS A 11 CG CD CE NZ
REMARK 470 GLU A 53 CG CD OE1 OE2
REMARK 470 GLN A 102 CG CD OE1 NE2
REMARK 470 LYS A 112 CG CD CE NZ
REMARK 470 ARG B 6 CG CD NE CZ NH1 NH2
REMARK 470 HIS B 73 CG ND1 CD2 CE1 NE2
REMARK 470 GLU B 110 CG CD OE1 OE2
REMARK 470 LYS B 112 CG CD CE NZ
REMARK 470 ASP C 10 CG OD1 OD2
REMARK 470 LYS C 11 CG CD CE NZ
REMARK 470 PRO C 20 CG CD
REMARK 470 ASN C 30 CG OD1 ND2
REMARK 470 GLU C 42 CG CD OE1 OE2
REMARK 470 ARG C 44 CG CD NE CZ NH1 NH2
REMARK 470 GLU C 53 CG CD OE1 OE2
REMARK 470 LYS C 65 CG CD CE NZ
REMARK 470 GLN C 67 CG CD OE1 NE2
REMARK 470 THR C 72 OG1 CG2
REMARK 470 GLN C 88 CG CD OE1 NE2
REMARK 470 GLN C 102 CG CD OE1 NE2
REMARK 470 ARG C 103 CG CD NE CZ NH1 NH2
REMARK 470 GLU C 104 CG CD OE1 OE2
REMARK 470 LYS C 112 CG CD CE NZ
REMARK 470 LYS C 128 CG CD CE NZ
REMARK 470 PHE C 144 CG CD1 CD2 CE1 CE2 CZ
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 ARG A 32 146.85 -170.62
REMARK 500 LEU A 36 135.91 -170.62
REMARK 500 ASN A 46 18.09 55.21
REMARK 500 ALA A 145 98.12 -51.27
REMARK 500 GLU A 146 151.04 70.02
REMARK 500 LEU B 36 133.56 -178.07
REMARK 500 ASN C 39 -80.35 -144.58
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 CL C 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue A6Y C 202
DBREF 6OOZ A 1 157 UNP P01375 TNFA_HUMAN 77 233
DBREF 6OOZ B 1 157 UNP P01375 TNFA_HUMAN 77 233
DBREF 6OOZ C 1 157 UNP P01375 TNFA_HUMAN 77 233
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 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 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 B 157 VAL ARG SER SER SER ARG THR PRO SER ASP LYS 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 LYS
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 LYS VAL
SEQRES 8 B 157 ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG GLU
SEQRES 9 B 157 THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU PRO
SEQRES 10 B 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS 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 LYS PRO VAL
SEQRES 2 C 157 ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN LEU
SEQRES 3 C 157 GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA ASN
SEQRES 4 C 157 GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SER
SEQRES 5 C 157 GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE LYS
SEQRES 6 C 157 GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR HIS
SEQRES 7 C 157 THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS VAL
SEQRES 8 C 157 ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG GLU
SEQRES 9 C 157 THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU PRO
SEQRES 10 C 157 ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY ASP
SEQRES 11 C 157 ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU ASP
SEQRES 12 C 157 PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE ALA
SEQRES 13 C 157 LEU
HET CL C 201 1
HET A6Y C 202 26
HETNAM CL CHLORIDE ION
HETNAM A6Y (S)-{1-[(2,5-DIMETHYLPHENYL)METHYL]-1H-BENZIMIDAZOL-2-
HETNAM 2 A6Y YL}(PYRIDIN-4-YL)METHANOL
FORMUL 4 CL CL 1-
FORMUL 5 A6Y C22 H21 N3 O
FORMUL 6 HOH *44(H2 O)
HELIX 1 AA1 ARG A 138 LEU A 142 5 5
HELIX 2 AA2 ARG B 138 LEU B 142 5 5
HELIX 3 AA3 ARG C 138 LEU C 142 5 5
SHEET 1 AA1 3 TRP A 28 LEU A 29 0
SHEET 2 AA1 3 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29
SHEET 3 AA1 3 LEU A 36 ALA A 38 -1 O ALA A 38 N VAL A 13
SHEET 1 AA2 5 TRP A 28 LEU A 29 0
SHEET 2 AA2 5 VAL A 13 ALA A 18 -1 N VAL A 17 O LEU A 29
SHEET 3 AA2 5 TYR A 151 ALA A 156 -1 O PHE A 152 N VAL A 16
SHEET 4 AA2 5 GLY A 54 GLN A 67 -1 N LEU A 57 O ILE A 155
SHEET 5 AA2 5 PRO A 113 LEU A 126 -1 O TRP A 114 N GLY A 66
SHEET 1 AA3 5 GLU A 42 ARG A 44 0
SHEET 2 AA3 5 GLN A 47 VAL A 49 -1 O VAL A 49 N GLU A 42
SHEET 3 AA3 5 ARG A 131 ILE A 136 -1 O LEU A 132 N LEU A 48
SHEET 4 AA3 5 LEU A 76 ALA A 84 -1 N THR A 79 O GLU A 135
SHEET 5 AA3 5 TYR A 87 LYS A 98 -1 O VAL A 91 N ARG A 82
SHEET 1 AA4 3 TRP B 28 LEU B 29 0
SHEET 2 AA4 3 VAL B 13 ALA B 18 -1 N VAL B 17 O LEU B 29
SHEET 3 AA4 3 LEU B 36 ALA B 38 -1 O LEU B 36 N HIS B 15
SHEET 1 AA5 5 TRP B 28 LEU B 29 0
SHEET 2 AA5 5 VAL B 13 ALA B 18 -1 N VAL B 17 O LEU B 29
SHEET 3 AA5 5 TYR B 151 ALA B 156 -1 O PHE B 152 N VAL B 16
SHEET 4 AA5 5 GLY B 54 GLN B 67 -1 N LEU B 57 O ILE B 155
SHEET 5 AA5 5 PRO B 113 LEU B 126 -1 O ILE B 118 N VAL B 62
SHEET 1 AA6 5 GLU B 42 ARG B 44 0
SHEET 2 AA6 5 GLN B 47 VAL B 49 -1 O GLN B 47 N ARG B 44
SHEET 3 AA6 5 ARG B 131 ILE B 136 -1 O LEU B 132 N LEU B 48
SHEET 4 AA6 5 LEU B 76 ILE B 83 -1 N THR B 79 O GLU B 135
SHEET 5 AA6 5 LYS B 90 LYS B 98 -1 O VAL B 91 N ARG B 82
SHEET 1 AA7 5 TRP C 28 LEU C 29 0
SHEET 2 AA7 5 VAL C 13 ALA C 18 -1 N VAL C 17 O LEU C 29
SHEET 3 AA7 5 TYR C 151 ALA C 156 -1 O PHE C 152 N VAL C 16
SHEET 4 AA7 5 GLY C 54 GLY C 66 -1 N LEU C 57 O ILE C 155
SHEET 5 AA7 5 TRP C 114 LEU C 126 -1 O PHE C 124 N TYR C 56
SHEET 1 AA8 5 GLU C 42 ARG C 44 0
SHEET 2 AA8 5 GLN C 47 VAL C 49 -1 O VAL C 49 N GLU C 42
SHEET 3 AA8 5 ARG C 131 ILE C 136 -1 O LEU C 132 N LEU C 48
SHEET 4 AA8 5 LEU C 76 ILE C 83 -1 N ILE C 83 O ARG C 131
SHEET 5 AA8 5 LYS C 90 LYS C 98 -1 O LYS C 98 N LEU C 76
SSBOND 1 CYS A 69 CYS A 101 1555 1555 2.05
SSBOND 2 CYS B 69 CYS B 101 1555 1555 2.04
SSBOND 3 CYS C 69 CYS C 101 1555 1555 2.04
SITE 1 AC1 1 ASN C 92
SITE 1 AC2 10 LEU A 57 TYR A 119 TYR B 119 GLY B 121
SITE 2 AC2 10 GLY B 122 TYR C 59 SER C 60 TYR C 119
SITE 3 AC2 10 LEU C 120 TYR C 151
CRYST1 53.520 81.170 93.350 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 0.018685 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012320 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010712 0.00000