HEADER CYTOKINE 23-APR-19 6OOY
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,T.CESKA
REVDAT 4 13-NOV-24 6OOY 1 REMARK
REVDAT 3 03-APR-24 6OOY 1 REMARK
REVDAT 2 01-JAN-20 6OOY 1 JRNL
REVDAT 1 25-DEC-19 6OOY 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. 2.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0109
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) : 2.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 92.28
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 14708
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) : 0.205
REMARK 3 R VALUE (WORKING SET) : 0.201
REMARK 3 FREE R VALUE : 0.272
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 745
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) : 992
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.32
REMARK 3 BIN R VALUE (WORKING SET) : 0.2440
REMARK 3 BIN FREE R VALUE SET COUNT : 60
REMARK 3 BIN FREE R VALUE : 0.2990
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3181
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 28
REMARK 3 SOLVENT ATOMS : 83
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 33.95
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.62
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 14.83000
REMARK 3 B22 (A**2) : -7.16000
REMARK 3 B33 (A**2) : -7.67000
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): 0.227
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.188
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.491
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3291 ; 0.015 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2156 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4492 ; 1.559 ; 1.980
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5274 ; 0.878 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 409 ; 7.091 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;33.723 ;24.539
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 506 ;14.305 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;20.527 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 511 ; 0.089 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3650 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 635 ; 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): 2065 ; 0.843 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 835 ; 0.125 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3307 ; 1.568 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1226 ; 1.925 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1183 ; 3.118 ; 4.500
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 : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED
REMARK 4
REMARK 4 6OOY 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_1000241081.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-MAR-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 : 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) : 0.9795
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14744
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500
REMARK 200 RESOLUTION RANGE LOW (A) : 92.280
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.09100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000
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) : 2.57
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : 0.49000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000
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: RODS
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.55
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 13% MPD, 13% PEG 1000, 13% PEG 3350,
REMARK 280 0.1M HEPES, PH 8.0,VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 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 27.26500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.13000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.80000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.13000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.26500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.80000
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: 5450 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 17600 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 72
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 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 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 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 PRO C 8
REMARK 465 SER C 9
REMARK 465 ASP C 10
REMARK 465 PRO C 70
REMARK 465 SER C 71
REMARK 465 THR C 72
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 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 SER A 71 OG
REMARK 470 HIS A 73 CG ND1 CD2 CE1 NE2
REMARK 470 LYS A 112 CG CD CE NZ
REMARK 470 SER B 71 OG
REMARK 470 LYS B 112 CG CD CE NZ
REMARK 470 LYS C 11 CG CD CE NZ
REMARK 470 GLU C 23 CG CD OE1 OE2
REMARK 470 ARG C 31 CG CD NE CZ NH1 NH2
REMARK 470 ARG C 32 CG CD NE CZ NH1 NH2
REMARK 470 ASN C 34 CG OD1 ND2
REMARK 470 LYS C 65 CG CD CE NZ
REMARK 470 GLN C 67 CG CD OE1 NE2
REMARK 470 TYR C 87 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 LYS C 112 CG CD CE NZ
REMARK 470 PHE C 144 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 GLU C 146 CG CD OE1 OE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OH TYR A 87 O HOH A 301 2.12
REMARK 500
REMARK 500 REMARK: NULL
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 O HOH A 327 O HOH C 315 3554 2.14
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 TYR A 87 81.79 -161.72
REMARK 500 ASN C 34 59.66 70.54
REMARK 500 LEU C 36 171.08 -52.27
REMARK 500 LEU C 37 80.74 162.95
REMARK 500 SER C 86 -61.47 -103.08
REMARK 500 TYR C 87 -73.82 -43.84
REMARK 500 GLN C 88 0.06 107.80
REMARK 500 ARG C 138 74.36 -117.90
REMARK 500 GLU C 146 -144.56 -163.69
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 MRD A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue A7M C 201
DBREF 6OOY A 1 157 UNP P01375 TNFA_HUMAN 77 233
DBREF 6OOY B 1 157 UNP P01375 TNFA_HUMAN 77 233
DBREF 6OOY 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 MRD A 201 8
HET A7M C 201 20
HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL
HETNAM A7M {1-[(2,5-DIMETHYLPHENYL)METHYL]-1H-BENZIMIDAZOL-2-
HETNAM 2 A7M YL}METHANOL
FORMUL 4 MRD C6 H14 O2
FORMUL 5 A7M C17 H18 N2 O
FORMUL 6 HOH *83(H2 O)
HELIX 1 AA1 ARG B 138 LEU B 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 LEU A 36 N HIS A 15
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 GLU A 116 N PHE A 64
SHEET 1 AA3 5 GLU A 42 ARG A 44 0
SHEET 2 AA3 5 GLN A 47 VAL A 49 -1 O GLN A 47 N ARG A 44
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 ILE A 83 O ARG A 131
SHEET 5 AA3 5 TYR A 87 LYS A 98 -1 O LEU A 93 N ILE A 80
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 PHE B 124 N TYR B 56
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 3 TRP C 28 LEU C 29 0
SHEET 2 AA7 3 VAL C 13 ALA C 18 -1 N VAL C 17 O LEU C 29
SHEET 3 AA7 3 LEU C 37 ALA C 38 -1 O ALA C 38 N VAL C 13
SHEET 1 AA8 5 TRP C 28 LEU C 29 0
SHEET 2 AA8 5 VAL C 13 ALA C 18 -1 N VAL C 17 O LEU C 29
SHEET 3 AA8 5 TYR C 151 ALA C 156 -1 O PHE C 152 N VAL C 16
SHEET 4 AA8 5 GLY C 54 GLN C 67 -1 N TYR C 59 O GLY C 153
SHEET 5 AA8 5 PRO C 113 LEU C 126 -1 O GLY C 122 N ILE C 58
SHEET 1 AA9 5 GLU C 42 ARG C 44 0
SHEET 2 AA9 5 GLN C 47 VAL C 49 -1 O VAL C 49 N GLU C 42
SHEET 3 AA9 5 ARG C 131 ILE C 136 -1 O LEU C 132 N LEU C 48
SHEET 4 AA9 5 LEU C 76 ILE C 83 -1 N ILE C 83 O ARG C 131
SHEET 5 AA9 5 LYS C 90 LYS C 98 -1 O LEU C 93 N ILE C 80
SSBOND 1 CYS A 69 CYS A 101 1555 1555 1.91
SSBOND 2 CYS B 69 CYS B 101 1555 1555 1.95
SSBOND 3 CYS C 69 CYS C 101 1555 1555 2.01
SITE 1 AC1 6 SER A 60 LEU A 120 HOH A 302 TYR B 119
SITE 2 AC1 6 TYR C 119 A7M C 201
SITE 1 AC2 11 LEU A 57 TYR A 59 MRD A 201 TYR B 119
SITE 2 AC2 11 GLY B 121 GLY B 122 TYR C 59 SER C 60
SITE 3 AC2 11 TYR C 119 LEU C 120 TYR C 151
CRYST1 54.530 81.600 92.260 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 0.018339 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012255 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010839 0.00000