HEADER CYTOKINE 23-APR-19 6OP0 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,J.W.FAIRMAN,D.R.DAVIES,A.FOLEY,T.CESKA REVDAT 3 03-APR-24 6OP0 1 REMARK REVDAT 2 01-JAN-20 6OP0 1 JRNL REVDAT 1 25-DEC-19 6OP0 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. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 14153 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 721 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 870 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.4740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3083 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 67 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.37000 REMARK 3 B22 (A**2) : -1.60000 REMARK 3 B33 (A**2) : 0.23000 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): 1.025 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.309 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.143 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3187 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2044 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4357 ; 1.416 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4995 ; 0.823 ; 2.996 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 396 ; 7.566 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;35.571 ;24.538 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 464 ;13.588 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.573 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 501 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3538 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 616 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 6OP0 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_1000241113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-12 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) : 1.127 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 : 14153 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 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 : 6.300 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.52200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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 (%): 38.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23.2% PEG 3350, 5% MPD, 100 MM TRIS, REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, 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 27.08500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.08500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.99500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.08500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.08500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.99500 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: 4800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 SER A 0 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 SER B 0 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 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 SER C 0 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 20 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 ALA C 38 REMARK 465 ASN C 39 REMARK 465 SER C 86 REMARK 465 TYR C 87 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 PHE C 144 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 SER A 71 OG REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 GLN A 102 CG CD OE1 NE2 REMARK 470 ARG A 103 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 104 CG CD OE1 OE2 REMARK 470 THR A 105 OG1 CG2 REMARK 470 PRO A 106 CG CD REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 GLU A 146 CG CD OE1 OE2 REMARK 470 ARG B 44 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 LYS C 11 CG CD CE NZ REMARK 470 GLU C 23 CG CD OE1 OE2 REMARK 470 GLN C 27 CG CD OE1 NE2 REMARK 470 LEU C 29 CG CD1 CD2 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 LYS C 65 CG CD CE NZ REMARK 470 GLN C 67 CG CD OE1 NE2 REMARK 470 SER C 71 OG REMARK 470 THR C 72 OG1 CG2 REMARK 470 GLN C 88 CG CD OE1 NE2 REMARK 470 LYS C 112 CG CD CE NZ REMARK 470 LYS C 128 CG CD CE NZ REMARK 470 ARG C 131 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP B 28 CE2 TRP B 28 CD2 0.076 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 PRO A 8 154.01 -49.53 REMARK 500 TYR A 87 87.69 -161.05 REMARK 500 LEU B 36 128.55 -171.77 REMARK 500 HIS C 15 102.38 -160.63 REMARK 500 LEU C 43 79.28 -114.05 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 A7A C 201 DBREF 6OP0 A 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 6OP0 B 1 157 UNP P01375 TNFA_HUMAN 77 233 DBREF 6OP0 C 1 157 UNP P01375 TNFA_HUMAN 77 233 SEQADV 6OP0 SER A 0 UNP P01375 EXPRESSION TAG SEQADV 6OP0 SER B 0 UNP P01375 EXPRESSION TAG SEQADV 6OP0 SER C 0 UNP P01375 EXPRESSION TAG SEQRES 1 A 158 SER VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 A 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 A 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 A 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 A 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 A 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 A 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 A 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 A 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 A 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 A 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 A 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 A 158 ALA LEU SEQRES 1 B 158 SER VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 B 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 B 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 B 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 B 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 B 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 B 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 B 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 B 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 B 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 B 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 B 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 B 158 ALA LEU SEQRES 1 C 158 SER VAL ARG SER SER SER ARG THR PRO SER ASP LYS PRO SEQRES 2 C 158 VAL ALA HIS VAL VAL ALA ASN PRO GLN ALA GLU GLY GLN SEQRES 3 C 158 LEU GLN TRP LEU ASN ARG ARG ALA ASN ALA LEU LEU ALA SEQRES 4 C 158 ASN GLY VAL GLU LEU ARG ASP ASN GLN LEU VAL VAL PRO SEQRES 5 C 158 SER GLU GLY LEU TYR LEU ILE TYR SER GLN VAL LEU PHE SEQRES 6 C 158 LYS GLY GLN GLY CYS PRO SER THR HIS VAL LEU LEU THR SEQRES 7 C 158 HIS THR ILE SER ARG ILE ALA VAL SER TYR GLN THR LYS SEQRES 8 C 158 VAL ASN LEU LEU SER ALA ILE LYS SER PRO CYS GLN ARG SEQRES 9 C 158 GLU THR PRO GLU GLY ALA GLU ALA LYS PRO TRP TYR GLU SEQRES 10 C 158 PRO ILE TYR LEU GLY GLY VAL PHE GLN LEU GLU LYS GLY SEQRES 11 C 158 ASP ARG LEU SER ALA GLU ILE ASN ARG PRO ASP TYR LEU SEQRES 12 C 158 ASP PHE ALA GLU SER GLY GLN VAL TYR PHE GLY ILE ILE SEQRES 13 C 158 ALA LEU HET A7A C 201 32 HETNAM A7A (R)-{1-[(2,5-DIMETHYLPHENYL)METHYL]-6-(1-METHYL-1H- HETNAM 2 A7A PYRAZOL-4-YL)-1H-BENZIMIDAZOL-2-YL}(PYRIDIN-4-YL) HETNAM 3 A7A METHANOL FORMUL 4 A7A C26 H25 N5 O FORMUL 5 HOH *67(H2 O) HELIX 1 AA1 ARG A 138 LEU A 142 5 5 HELIX 2 AA2 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 TYR A 59 O GLY A 153 SHEET 5 AA2 5 PRO A 113 LEU A 126 -1 O GLY A 122 N ILE A 58 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 THR A 79 O GLU A 135 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 VAL B 49 N GLU B 42 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 4 VAL C 13 VAL C 17 0 SHEET 2 AA7 4 TYR C 151 ALA C 156 -1 O PHE C 152 N VAL C 16 SHEET 3 AA7 4 GLY C 54 GLN C 67 -1 N LEU C 57 O ILE C 155 SHEET 4 AA7 4 PRO C 113 LEU C 126 -1 O GLY C 122 N ILE C 58 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 LEU C 93 N ILE C 80 SSBOND 1 CYS A 69 CYS A 101 1555 1555 2.09 SSBOND 2 CYS B 69 CYS B 101 1555 1555 2.06 SSBOND 3 CYS C 69 CYS C 101 1555 1555 2.04 SITE 1 AC1 14 LEU A 57 TYR A 59 TYR A 119 ILE A 155 SITE 2 AC1 14 TYR B 119 GLY B 121 GLY B 122 LEU C 57 SITE 3 AC1 14 TYR C 59 SER C 60 TYR C 119 LEU C 120 SITE 4 AC1 14 TYR C 151 ILE C 155 CRYST1 54.170 81.990 94.170 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 0.018460 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010619 0.00000