PDB Short entry for 2AZ5 HEADER CYTOKINE 09-SEP-05 2AZ5 TITLE CRYSTAL STRUCTURE OF TNF-ALPHA WITH A SMALL MOLECULE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR (TNF-ALPHA) (TUMOR NECROSIS FACTOR COMPND 3 LIGAND SUPERFAMILY MEMBER 2) (TNF-A) (CACHECTIN) [CONTAINS: TUMOR COMPND 4 NECROSIS FACTOR, MEMBRANE FORM; TUMOR NECROSIS FACTOR, SOLUBLE FORM]; COMPND 5 CHAIN: A, B, C, D; 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 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 INHIBITOR, KEYWDS 2 CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR M.M.HE REVDAT 6 23-AUG-23 2AZ5 1 REMARK REVDAT 5 07-FEB-18 2AZ5 1 REMARK 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,A.C.BRAISTED, JRNL AUTH 2 A.WHITTY,M.T.CANCILLA,J.WANG,A.A.LUGOVSKOY,J.C.YOBURN, JRNL AUTH 3 A.D.FUNG,G.FARRINGTON,J.K.ELDREDGE,E.S.DAY,L.A.CRUZ, JRNL AUTH 4 T.G.CACHERO,S.K.MILLER,J.E.FRIEDMAN,I.C.CHOONG, JRNL AUTH 5 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 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1976 ; 3.598 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1649 ; 5.359 ; 5.000 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 : 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034476. 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 293K 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 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