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 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 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 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