PDB Short entry for 1D0G HEADER APOPTOSIS 09-SEP-99 1D0G TITLE CRYSTAL STRUCTURE OF DEATH RECEPTOR 5 (DR5) BOUND TO APO2L/TRAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEATH RECEPTOR-5; COMPND 3 CHAIN: R, S, T; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN RESIDUES 1-130; COMPND 5 SYNONYM: DR-5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: APOPTOSIS-2 LIGAND; COMPND 9 CHAIN: A, B, D; COMPND 10 FRAGMENT: RESIDUES 114-281; COMPND 11 SYNONYM: TRAIL, APO2L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 10469; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: BACULOVIRUS WITH POLYHEDRIN PROMOTER; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: BACTERIA; SOURCE 13 EXPRESSION_SYSTEM_COMMON: EUBACTERIA; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 2; SOURCE 15 EXPRESSION_SYSTEM_VECTOR: AP PROMOTER KEYWDS APOPTOSIS, BINDING AND SPECIFICITY, LIGAND-RECEPTOR COMPLEX, TNF KEYWDS 2 RECEPTOR FAMILY EXPDTA X-RAY DIFFRACTION AUTHOR S.G.HYMOWITZ,H.W.CHRISTINGER,G.FUH,M.P.O'CONNELL,R.F.KELLEY, AUTHOR 2 A.ASHKENAZI,A.M.DE VOS REVDAT 6 31-JAN-18 1D0G 1 REMARK REVDAT 5 24-FEB-09 1D0G 1 VERSN REVDAT 4 01-MAR-05 1D0G 1 DBREF REVDAT 3 01-APR-03 1D0G 1 JRNL REVDAT 2 10-NOV-99 1D0G 1 SHEET COMPND JRNL REMARK REVDAT 1 22-OCT-99 1D0G 0 JRNL AUTH S.G.HYMOWITZ,H.W.CHRISTINGER,G.FUH,M.ULTSCH,M.O'CONNELL, JRNL AUTH 2 R.F.KELLEY,A.ASHKENAZI,A.M.DE VOS JRNL TITL TRIGGERING CELL DEATH: THE CRYSTAL STRUCTURE OF APO2L/TRAIL JRNL TITL 2 IN A COMPLEX WITH DEATH RECEPTOR 5. JRNL REF MOL.CELL V. 4 563 1999 JRNL REFN ISSN 1097-2765 JRNL PMID 10549288 JRNL DOI 10.1016/S1097-2765(00)80207-5 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.200 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 38850 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 SET) : 0.222 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 3818 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5614 REMARK 3 BIN R VALUE (WORKING SET) : 0.3190 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 0.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 584 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6269 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 284 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.43000 REMARK 3 B22 (A**2) : 0.61000 REMARK 3 B33 (A**2) : 0.82000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.36 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.500 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.230 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.600 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.010 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED MAXIMUM LIKELIHOOD TARGET REMARK 4 REMARK 4 1D0G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 93 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) : 1.08 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38908 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG8K, 10% ETHYLENE GLYCOL, 0.2M REMARK 280 AMMONIUM SULFACE, 0.1M TRIS-HCL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 19K, TEMPERATURE 292.0K 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 33.40900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.40350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.50950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.40350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.40900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.50950 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS S HETEROHEXAMER CONSTRUCTUCTED REMARK 300 OF A TRIMER OF CHAINS A,B, AND D. CHAINS R,S,T BIND TO THE REMARK 300 INTERFACES BETWEEN CHAINS A,B,D. 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: R, S, T, A, B, 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 ALA R 1 REMARK 465 LEU R 2 REMARK 465 ILE R 3 REMARK 465 THR R 4 REMARK 465 GLN R 5 REMARK 465 GLN R 6 REMARK 465 ASP R 7 REMARK 465 LEU R 8 REMARK 465 ALA R 9 REMARK 465 PRO R 10 REMARK 465 GLN R 11 REMARK 465 GLN R 12 REMARK 465 ARG R 13 REMARK 465 ALA R 14 REMARK 465 ALA R 15 REMARK 465 PRO R 16 REMARK 465 GLN R 17 REMARK 465 GLN R 18 REMARK 465 LYS R 19 REMARK 465 ARG R 20 REMARK 465 GLU R 129 REMARK 465 SER R 130 REMARK 465 ALA S 1 REMARK 465 LEU S 2 REMARK 465 ILE S 3 REMARK 465 THR S 4 REMARK 465 GLN S 5 REMARK 465 GLN S 6 REMARK 465 ASP S 7 REMARK 465 LEU S 8 REMARK 465 ALA S 9 REMARK 465 PRO S 10 REMARK 465 GLN S 11 REMARK 465 GLN S 12 REMARK 465 ARG S 13 REMARK 465 ALA S 14 REMARK 465 ALA S 15 REMARK 465 PRO S 16 REMARK 465 GLN S 17 REMARK 465 GLN S 18 REMARK 465 LYS S 19 REMARK 465 ARG S 20 REMARK 465 ALA T 1 REMARK 465 LEU T 2 REMARK 465 ILE T 3 REMARK 465 THR T 4 REMARK 465 GLN T 5 REMARK 465 GLN T 6 REMARK 465 ASP T 7 REMARK 465 LEU T 8 REMARK 465 ALA T 9 REMARK 465 PRO T 10 REMARK 465 GLN T 11 REMARK 465 GLN T 12 REMARK 465 ARG T 13 REMARK 465 ALA T 14 REMARK 465 ALA T 15 REMARK 465 PRO T 16 REMARK 465 GLN T 17 REMARK 465 GLN T 18 REMARK 465 LYS T 19 REMARK 465 ARG T 20 REMARK 465 VAL A 114 REMARK 465 ARG A 115 REMARK 465 GLU A 116 REMARK 465 ARG A 117 REMARK 465 GLY A 118 REMARK 465 ARG A 132 REMARK 465 SER A 133 REMARK 465 ASN A 134 REMARK 465 THR A 135 REMARK 465 LEU A 136 REMARK 465 SER A 137 REMARK 465 SER A 138 REMARK 465 PRO A 139 REMARK 465 ASN A 140 REMARK 465 SER A 141 REMARK 465 LYS A 142 REMARK 465 ASN A 143 REMARK 465 VAL B 114 REMARK 465 ARG B 115 REMARK 465 GLU B 116 REMARK 465 ARG B 117 REMARK 465 GLY B 118 REMARK 465 ARG B 132 REMARK 465 SER B 133 REMARK 465 ASN B 134 REMARK 465 THR B 135 REMARK 465 LEU B 136 REMARK 465 SER B 137 REMARK 465 SER B 138 REMARK 465 PRO B 139 REMARK 465 ASN B 140 REMARK 465 SER B 141 REMARK 465 LYS B 142 REMARK 465 ASN B 143 REMARK 465 VAL D 114 REMARK 465 ARG D 115 REMARK 465 GLU D 116 REMARK 465 ARG D 117 REMARK 465 GLY D 118 REMARK 465 ARG D 132 REMARK 465 SER D 133 REMARK 465 ASN D 134 REMARK 465 THR D 135 REMARK 465 LEU D 136 REMARK 465 SER D 137 REMARK 465 SER D 138 REMARK 465 PRO D 139 REMARK 465 ASN D 140 REMARK 465 SER D 141 REMARK 465 LYS D 142 REMARK 465 ASN D 143 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 PRO A 119 CB CG CD REMARK 480 GLU A 144 CB CG CD OE1 OE2 REMARK 480 PRO B 119 CB CG CD REMARK 480 ARG B 130 CB CG CD NE CZ NH1 NH2 REMARK 480 GLU B 144 CB CG CD OE1 OE2 REMARK 480 LYS B 145 N REMARK 480 PRO D 119 CB CG CD REMARK 480 ARG D 130 CB CG CD NE CZ NH1 NH2 REMARK 480 GLY D 131 N REMARK 480 GLU D 144 CB CG CD OE1 OE2 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 GLU A 198 CG GLU A 198 CD 0.199 REMARK 500 GLU A 198 CD GLU A 198 OE1 0.110 REMARK 500 GLU A 198 CD GLU A 198 OE2 0.076 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 GLU T 129 N - CA - C ANGL. DEV. = -17.9 DEGREES REMARK 500 ARG B 158 CG - CD - NE ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG B 158 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 158 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES 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 R 108 175.75 -53.64 REMARK 500 VAL S 114 -32.44 -133.88 REMARK 500 GLU T 129 -71.09 -108.88 REMARK 500 ARG A 130 97.67 -69.08 REMARK 500 SER A 157 150.72 132.30 REMARK 500 ASN A 166 33.48 78.01 REMARK 500 GLN A 193 69.49 -113.50 REMARK 500 ILE A 196 102.42 -59.16 REMARK 500 GLU A 198 -76.01 -58.24 REMARK 500 ASN A 199 46.76 -85.98 REMARK 500 THR A 214 -161.21 -119.78 REMARK 500 SER A 215 42.02 -80.95 REMARK 500 GLN B 193 75.07 -115.19 REMARK 500 ILE B 196 96.16 -57.80 REMARK 500 LYS B 197 92.69 -68.97 REMARK 500 GLU B 198 -92.96 -0.82 REMARK 500 THR B 214 -161.80 -119.73 REMARK 500 SER B 215 47.94 -78.46 REMARK 500 ASN D 166 34.15 75.45 REMARK 500 GLN D 193 78.67 -117.07 REMARK 500 ILE D 196 91.79 -61.13 REMARK 500 GLU D 198 -84.52 -77.67 REMARK 500 ASN D 199 47.11 -78.29 REMARK 500 THR D 214 -164.74 -115.60 REMARK 500 SER D 215 46.50 -77.74 REMARK 500 ASN D 253 5.38 81.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 230 SG REMARK 620 2 CL B 400 CL 106.6 REMARK 620 3 CYS D 230 SG 116.0 104.3 REMARK 620 4 CYS B 230 SG 108.1 108.7 112.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 400 DBREF 1D0G A 114 281 UNP P50591 TNF10_HUMAN 114 281 DBREF 1D0G B 114 281 UNP P50591 TNF10_HUMAN 114 281 DBREF 1D0G D 114 281 UNP P50591 TNF10_HUMAN 114 281 DBREF 1D0G R 1 130 UNP O14763 TR10B_HUMAN 54 183 DBREF 1D0G S 1 130 UNP O14763 TR10B_HUMAN 54 183 DBREF 1D0G T 1 130 UNP O14763 TR10B_HUMAN 54 183 SEQRES 1 R 130 ALA LEU ILE THR GLN GLN ASP LEU ALA PRO GLN GLN ARG SEQRES 2 R 130 ALA ALA PRO GLN GLN LYS ARG SER SER PRO SER GLU GLY SEQRES 3 R 130 LEU CYS PRO PRO GLY HIS HIS ILE SER GLU ASP GLY ARG SEQRES 4 R 130 ASP CYS ILE SER CYS LYS TYR GLY GLN ASP TYR SER THR SEQRES 5 R 130 HIS TRP ASN ASP LEU LEU PHE CYS LEU ARG CYS THR ARG SEQRES 6 R 130 CYS ASP SER GLY GLU VAL GLU LEU SER PRO CYS THR THR SEQRES 7 R 130 THR ARG ASN THR VAL CYS GLN CYS GLU GLU GLY THR PHE SEQRES 8 R 130 ARG GLU GLU ASP SER PRO GLU MET CYS ARG LYS CYS ARG SEQRES 9 R 130 THR GLY CYS PRO ARG GLY MET VAL LYS VAL GLY ASP CYS SEQRES 10 R 130 THR PRO TRP SER ASP ILE GLU CYS VAL HIS LYS GLU SER SEQRES 1 S 130 ALA LEU ILE THR GLN GLN ASP LEU ALA PRO GLN GLN ARG SEQRES 2 S 130 ALA ALA PRO GLN GLN LYS ARG SER SER PRO SER GLU GLY SEQRES 3 S 130 LEU CYS PRO PRO GLY HIS HIS ILE SER GLU ASP GLY ARG SEQRES 4 S 130 ASP CYS ILE SER CYS LYS TYR GLY GLN ASP TYR SER THR SEQRES 5 S 130 HIS TRP ASN ASP LEU LEU PHE CYS LEU ARG CYS THR ARG SEQRES 6 S 130 CYS ASP SER GLY GLU VAL GLU LEU SER PRO CYS THR THR SEQRES 7 S 130 THR ARG ASN THR VAL CYS GLN CYS GLU GLU GLY THR PHE SEQRES 8 S 130 ARG GLU GLU ASP SER PRO GLU MET CYS ARG LYS CYS ARG SEQRES 9 S 130 THR GLY CYS PRO ARG GLY MET VAL LYS VAL GLY ASP CYS SEQRES 10 S 130 THR PRO TRP SER ASP ILE GLU CYS VAL HIS LYS GLU SER SEQRES 1 T 130 ALA LEU ILE THR GLN GLN ASP LEU ALA PRO GLN GLN ARG SEQRES 2 T 130 ALA ALA PRO GLN GLN LYS ARG SER SER PRO SER GLU GLY SEQRES 3 T 130 LEU CYS PRO PRO GLY HIS HIS ILE SER GLU ASP GLY ARG SEQRES 4 T 130 ASP CYS ILE SER CYS LYS TYR GLY GLN ASP TYR SER THR SEQRES 5 T 130 HIS TRP ASN ASP LEU LEU PHE CYS LEU ARG CYS THR ARG SEQRES 6 T 130 CYS ASP SER GLY GLU VAL GLU LEU SER PRO CYS THR THR SEQRES 7 T 130 THR ARG ASN THR VAL CYS GLN CYS GLU GLU GLY THR PHE SEQRES 8 T 130 ARG GLU GLU ASP SER PRO GLU MET CYS ARG LYS CYS ARG SEQRES 9 T 130 THR GLY CYS PRO ARG GLY MET VAL LYS VAL GLY ASP CYS SEQRES 10 T 130 THR PRO TRP SER ASP ILE GLU CYS VAL HIS LYS GLU SER SEQRES 1 A 168 VAL ARG GLU ARG GLY PRO GLN ARG VAL ALA ALA HIS ILE SEQRES 2 A 168 THR GLY THR ARG GLY ARG SER ASN THR LEU SER SER PRO SEQRES 3 A 168 ASN SER LYS ASN GLU LYS ALA LEU GLY ARG LYS ILE ASN SEQRES 4 A 168 SER TRP GLU SER SER ARG SER GLY HIS SER PHE LEU SER SEQRES 5 A 168 ASN LEU HIS LEU ARG ASN GLY GLU LEU VAL ILE HIS GLU SEQRES 6 A 168 LYS GLY PHE TYR TYR ILE TYR SER GLN THR TYR PHE ARG SEQRES 7 A 168 PHE GLN GLU GLU ILE LYS GLU ASN THR LYS ASN ASP LYS SEQRES 8 A 168 GLN MET VAL GLN TYR ILE TYR LYS TYR THR SER TYR PRO SEQRES 9 A 168 ASP PRO ILE LEU LEU MET LYS SER ALA ARG ASN SER CYS SEQRES 10 A 168 TRP SER LYS ASP ALA GLU TYR GLY LEU TYR SER ILE TYR SEQRES 11 A 168 GLN GLY GLY ILE PHE GLU LEU LYS GLU ASN ASP ARG ILE SEQRES 12 A 168 PHE VAL SER VAL THR ASN GLU HIS LEU ILE ASP MET ASP SEQRES 13 A 168 HIS GLU ALA SER PHE PHE GLY ALA PHE LEU VAL GLY SEQRES 1 B 168 VAL ARG GLU ARG GLY PRO GLN ARG VAL ALA ALA HIS ILE SEQRES 2 B 168 THR GLY THR ARG GLY ARG SER ASN THR LEU SER SER PRO SEQRES 3 B 168 ASN SER LYS ASN GLU LYS ALA LEU GLY ARG LYS ILE ASN SEQRES 4 B 168 SER TRP GLU SER SER ARG SER GLY HIS SER PHE LEU SER SEQRES 5 B 168 ASN LEU HIS LEU ARG ASN GLY GLU LEU VAL ILE HIS GLU SEQRES 6 B 168 LYS GLY PHE TYR TYR ILE TYR SER GLN THR TYR PHE ARG SEQRES 7 B 168 PHE GLN GLU GLU ILE LYS GLU ASN THR LYS ASN ASP LYS SEQRES 8 B 168 GLN MET VAL GLN TYR ILE TYR LYS TYR THR SER TYR PRO SEQRES 9 B 168 ASP PRO ILE LEU LEU MET LYS SER ALA ARG ASN SER CYS SEQRES 10 B 168 TRP SER LYS ASP ALA GLU TYR GLY LEU TYR SER ILE TYR SEQRES 11 B 168 GLN GLY GLY ILE PHE GLU LEU LYS GLU ASN ASP ARG ILE SEQRES 12 B 168 PHE VAL SER VAL THR ASN GLU HIS LEU ILE ASP MET ASP SEQRES 13 B 168 HIS GLU ALA SER PHE PHE GLY ALA PHE LEU VAL GLY SEQRES 1 D 168 VAL ARG GLU ARG GLY PRO GLN ARG VAL ALA ALA HIS ILE SEQRES 2 D 168 THR GLY THR ARG GLY ARG SER ASN THR LEU SER SER PRO SEQRES 3 D 168 ASN SER LYS ASN GLU LYS ALA LEU GLY ARG LYS ILE ASN SEQRES 4 D 168 SER TRP GLU SER SER ARG SER GLY HIS SER PHE LEU SER SEQRES 5 D 168 ASN LEU HIS LEU ARG ASN GLY GLU LEU VAL ILE HIS GLU SEQRES 6 D 168 LYS GLY PHE TYR TYR ILE TYR SER GLN THR TYR PHE ARG SEQRES 7 D 168 PHE GLN GLU GLU ILE LYS GLU ASN THR LYS ASN ASP LYS SEQRES 8 D 168 GLN MET VAL GLN TYR ILE TYR LYS TYR THR SER TYR PRO SEQRES 9 D 168 ASP PRO ILE LEU LEU MET LYS SER ALA ARG ASN SER CYS SEQRES 10 D 168 TRP SER LYS ASP ALA GLU TYR GLY LEU TYR SER ILE TYR SEQRES 11 D 168 GLN GLY GLY ILE PHE GLU LEU LYS GLU ASN ASP ARG ILE SEQRES 12 D 168 PHE VAL SER VAL THR ASN GLU HIS LEU ILE ASP MET ASP SEQRES 13 D 168 HIS GLU ALA SER PHE PHE GLY ALA PHE LEU VAL GLY HET ZN A 300 1 HET CL B 400 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 7 ZN ZN 2+ FORMUL 8 CL CL 1- FORMUL 9 HOH *284(H2 O) HELIX 1 1 ASN A 262 LEU A 265 5 4 HELIX 2 2 SER B 157 HIS B 161 5 5 HELIX 3 3 ASN B 262 HIS B 264 5 3 HELIX 4 4 SER D 157 HIS D 161 5 5 HELIX 5 5 ASN D 262 HIS D 264 5 3 SHEET 1 A 2 HIS R 32 ILE R 34 0 SHEET 2 A 2 CYS R 41 SER R 43 -1 N ILE R 42 O HIS R 33 SHEET 1 B 2 ASP R 49 TYR R 50 0 SHEET 2 B 2 LEU R 61 ARG R 62 -1 O LEU R 61 N TYR R 50 SHEET 1 C 2 GLU R 70 SER R 74 0 SHEET 2 C 2 VAL R 83 CYS R 86 -1 O VAL R 83 N LEU R 73 SHEET 1 D 2 THR R 90 GLU R 93 0 SHEET 2 D 2 SER R 96 LYS R 102 -1 N SER R 96 O GLU R 93 SHEET 1 E 2 VAL R 112 GLY R 115 0 SHEET 2 E 2 GLU R 124 VAL R 126 -1 O GLU R 124 N VAL R 114 SHEET 1 F 2 HIS S 32 ILE S 34 0 SHEET 2 F 2 CYS S 41 SER S 43 -1 N ILE S 42 O HIS S 33 SHEET 1 G 2 ASP S 49 TYR S 50 0 SHEET 2 G 2 LEU S 61 ARG S 62 -1 N LEU S 61 O TYR S 50 SHEET 1 H 2 GLU S 70 SER S 74 0 SHEET 2 H 2 VAL S 83 CYS S 86 -1 N VAL S 83 O SER S 74 SHEET 1 I 2 THR S 90 GLU S 93 0 SHEET 2 I 2 SER S 96 LYS S 102 -1 N SER S 96 O GLU S 93 SHEET 1 J 2 MET S 111 GLY S 115 0 SHEET 2 J 2 GLU S 124 HIS S 127 -1 N GLU S 124 O GLY S 115 SHEET 1 K 2 HIS T 32 ILE T 34 0 SHEET 2 K 2 CYS T 41 SER T 43 -1 N ILE T 42 O HIS T 33 SHEET 1 L 2 ASP T 49 TYR T 50 0 SHEET 2 L 2 LEU T 61 ARG T 62 -1 N LEU T 61 O TYR T 50 SHEET 1 M 2 GLU T 70 SER T 74 0 SHEET 2 M 2 VAL T 83 CYS T 86 -1 N VAL T 83 O SER T 74 SHEET 1 N 2 THR T 90 PHE T 91 0 SHEET 2 N 2 ARG T 101 LYS T 102 -1 N ARG T 101 O PHE T 91 SHEET 1 O 2 MET T 111 GLY T 115 0 SHEET 2 O 2 GLU T 124 HIS T 127 -1 O GLU T 124 N VAL T 114 SHEET 1 P 5 PHE A 163 SER A 165 0 SHEET 2 P 5 ALA A 123 THR A 127 -1 O ALA A 123 N SER A 165 SHEET 3 P 5 PHE A 274 LEU A 279 -1 O PHE A 275 N ILE A 126 SHEET 4 P 5 GLY A 180 PHE A 192 -1 N TYR A 183 O PHE A 278 SHEET 5 P 5 GLY A 238 LEU A 250 -1 N GLY A 238 O PHE A 192 SHEET 1 Q 4 ILE A 220 ASN A 228 0 SHEET 2 Q 4 GLN A 205 TYR A 213 -1 N MET A 206 O ARG A 227 SHEET 3 Q 4 ARG A 255 VAL A 260 -1 O ARG A 255 N TYR A 213 SHEET 4 Q 4 ARG A 149 LYS A 150 -1 N ARG A 149 O VAL A 260 SHEET 1 Q1 5 ILE A 220 ASN A 228 0 SHEET 2 Q1 5 GLN A 205 TYR A 213 -1 N MET A 206 O ARG A 227 SHEET 3 Q1 5 ARG A 255 VAL A 260 -1 O ARG A 255 N TYR A 213 SHEET 4 Q1 5 GLU A 173 ILE A 176 -1 N LEU A 174 O ILE A 256 SHEET 5 Q1 5 LEU A 167 ARG A 170 -1 O HIS A 168 N VAL A 175 SHEET 1 R 5 PHE B 163 SER B 165 0 SHEET 2 R 5 ALA B 123 THR B 127 -1 O ALA B 123 N SER B 165 SHEET 3 R 5 PHE B 274 LEU B 279 -1 O PHE B 275 N ILE B 126 SHEET 4 R 5 GLY B 180 PHE B 192 -1 N TYR B 183 O PHE B 278 SHEET 5 R 5 GLY B 238 LEU B 250 -1 N GLY B 238 O PHE B 192 SHEET 1 S 4 ILE B 220 ASN B 228 0 SHEET 2 S 4 GLN B 205 TYR B 213 -1 N MET B 206 O ARG B 227 SHEET 3 S 4 ARG B 255 VAL B 260 -1 O ARG B 255 N TYR B 213 SHEET 4 S 4 ARG B 149 LYS B 150 -1 N ARG B 149 O VAL B 260 SHEET 1 S1 5 ILE B 220 ASN B 228 0 SHEET 2 S1 5 GLN B 205 TYR B 213 -1 N MET B 206 O ARG B 227 SHEET 3 S1 5 ARG B 255 VAL B 260 -1 O ARG B 255 N TYR B 213 SHEET 4 S1 5 GLU B 173 ILE B 176 -1 N LEU B 174 O ILE B 256 SHEET 5 S1 5 LEU B 167 ARG B 170 -1 O HIS B 168 N VAL B 175 SHEET 1 T 5 PHE D 163 SER D 165 0 SHEET 2 T 5 ALA D 123 THR D 127 -1 O ALA D 123 N SER D 165 SHEET 3 T 5 PHE D 274 LEU D 279 -1 O PHE D 275 N ILE D 126 SHEET 4 T 5 GLY D 180 PHE D 192 -1 N TYR D 183 O PHE D 278 SHEET 5 T 5 GLY D 238 LEU D 250 -1 N GLY D 238 O PHE D 192 SHEET 1 U 4 ILE D 220 ASN D 228 0 SHEET 2 U 4 GLN D 205 TYR D 213 -1 N MET D 206 O ARG D 227 SHEET 3 U 4 ARG D 255 VAL D 260 -1 O ARG D 255 N TYR D 213 SHEET 4 U 4 ARG D 149 LYS D 150 -1 N ARG D 149 O VAL D 260 SHEET 1 U1 5 ILE D 220 ASN D 228 0 SHEET 2 U1 5 GLN D 205 TYR D 213 -1 N MET D 206 O ARG D 227 SHEET 3 U1 5 ARG D 255 VAL D 260 -1 O ARG D 255 N TYR D 213 SHEET 4 U1 5 GLU D 173 ILE D 176 -1 N LEU D 174 O ILE D 256 SHEET 5 U1 5 LEU D 167 ARG D 170 -1 O HIS D 168 N VAL D 175 SSBOND 1 CYS R 28 CYS R 41 1555 1555 2.03 SSBOND 2 CYS R 44 CYS R 60 1555 1555 2.04 SSBOND 3 CYS R 63 CYS R 76 1555 1555 2.03 SSBOND 4 CYS R 66 CYS R 84 1555 1555 2.03 SSBOND 5 CYS R 86 CYS R 100 1555 1555 2.03 SSBOND 6 CYS R 103 CYS R 117 1555 1555 2.04 SSBOND 7 CYS R 107 CYS R 125 1555 1555 2.05 SSBOND 8 CYS S 28 CYS S 41 1555 1555 2.05 SSBOND 9 CYS S 44 CYS S 60 1555 1555 2.02 SSBOND 10 CYS S 63 CYS S 76 1555 1555 2.04 SSBOND 11 CYS S 66 CYS S 84 1555 1555 2.04 SSBOND 12 CYS S 86 CYS S 100 1555 1555 2.03 SSBOND 13 CYS S 103 CYS S 117 1555 1555 2.03 SSBOND 14 CYS S 107 CYS S 125 1555 1555 2.04 SSBOND 15 CYS T 28 CYS T 41 1555 1555 2.03 SSBOND 16 CYS T 44 CYS T 60 1555 1555 2.02 SSBOND 17 CYS T 63 CYS T 76 1555 1555 2.02 SSBOND 18 CYS T 66 CYS T 84 1555 1555 2.03 SSBOND 19 CYS T 86 CYS T 100 1555 1555 2.02 SSBOND 20 CYS T 103 CYS T 117 1555 1555 2.02 SSBOND 21 CYS T 107 CYS T 125 1555 1555 2.04 LINK ZN ZN A 300 SG CYS A 230 1555 1555 2.39 LINK ZN ZN A 300 CL CL B 400 1555 1555 2.35 LINK ZN ZN A 300 SG CYS D 230 1555 1555 2.42 LINK ZN ZN A 300 SG CYS B 230 1555 1555 2.34 SITE 1 AC1 4 CYS A 230 CYS B 230 CL B 400 CYS D 230 SITE 1 AC2 4 CYS A 230 ZN A 300 CYS B 230 CYS D 230 CRYST1 66.818 111.019 130.807 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 0.014970 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009010 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007640 0.00000