PDB Short entry for 4JJ7 HEADER HYDROLASE/HYDROLASE INHIBITOR 07-MAR-13 4JJ7 TITLE CASPASE-3 SPECIFIC UNNATURAL AMINO ACID-BASED PEPTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CASP-8, APOPTOTIC CYSTEINE PROTEASE, APOPTOTIC PROTEASE MCH- COMPND 5 5, CAP4, FADD-HOMOLOGOUS ICE/CED-3-LIKE PROTEASE, FADD-LIKE ICE, COMPND 6 FLICE, ICE-LIKE APOPTOTIC PROTEASE 5, MORT1-ASSOCIATED CED-3 HOMOLOG, COMPND 7 MACH, CASPASE-8 SUBUNIT P18, CASPASE-8 SUBUNIT P10; COMPND 8 EC: 3.4.22.61; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: CASPASE INHIBITOR; COMPND 12 CHAIN: B; COMPND 13 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: CASP8, CASP8 MCH5, MCH5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.J.VICKERS,G.E.GONZALEZ-PAEZ,D.W.WOLAN REVDAT 4 15-NOV-23 4JJ7 1 REMARK SEQADV LINK ATOM REVDAT 3 12-MAR-14 4JJ7 1 REMARK REVDAT 2 19-FEB-14 4JJ7 1 JRNL REVDAT 1 12-JUN-13 4JJ7 0 JRNL AUTH C.J.VICKERS,G.E.GONZALEZ-PAEZ,D.W.WOLAN JRNL TITL SELECTIVE DETECTION OF CASPASE-3 VERSUS CASPASE-7 USING JRNL TITL 2 ACTIVITY-BASED PROBES WITH KEY UNNATURAL AMINO ACIDS. JRNL REF ACS CHEM.BIOL. V. 8 1558 2013 JRNL REFN ISSN 1554-8929 JRNL PMID 23614665 JRNL DOI 10.1021/CB400209W REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 94058 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 4671 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.3696 - 3.6561 0.86 2590 124 0.1618 0.2046 REMARK 3 2 3.6561 - 2.9037 0.97 2505 136 0.1686 0.1699 REMARK 3 3 2.9037 - 2.5372 1.00 3152 178 0.1701 0.1835 REMARK 3 4 2.5372 - 2.3054 1.00 3171 161 0.1522 0.1759 REMARK 3 5 2.3054 - 2.1403 0.47 1483 76 0.1402 0.1507 REMARK 3 6 2.1403 - 2.0142 1.00 3126 166 0.1374 0.1487 REMARK 3 7 2.0142 - 1.9133 0.99 3106 173 0.1336 0.1616 REMARK 3 8 1.9133 - 1.8301 0.85 2642 162 0.1327 0.1499 REMARK 3 9 1.8301 - 1.7597 1.00 3120 147 0.1260 0.1528 REMARK 3 10 1.7597 - 1.6990 1.00 3062 186 0.1196 0.1387 REMARK 3 11 1.6990 - 1.6459 1.00 3132 167 0.1107 0.1227 REMARK 3 12 1.6459 - 1.5988 1.00 3106 158 0.1025 0.1400 REMARK 3 13 1.5988 - 1.5567 1.00 3092 176 0.0997 0.1273 REMARK 3 14 1.5567 - 1.5188 1.00 3099 171 0.0936 0.1169 REMARK 3 15 1.5188 - 1.4842 1.00 3085 140 0.0979 0.1240 REMARK 3 16 1.4842 - 1.4527 1.00 3119 162 0.1017 0.1359 REMARK 3 17 1.4527 - 1.4236 1.00 3058 173 0.1041 0.1383 REMARK 3 18 1.4236 - 1.3967 1.00 3077 146 0.0966 0.1319 REMARK 3 19 1.3967 - 1.3718 1.00 3133 170 0.0976 0.1086 REMARK 3 20 1.3718 - 1.3486 1.00 3088 176 0.1033 0.1244 REMARK 3 21 1.3486 - 1.3268 1.00 3060 182 0.1017 0.1328 REMARK 3 22 1.3268 - 1.3064 1.00 3051 165 0.1084 0.1462 REMARK 3 23 1.3064 - 1.2872 1.00 3103 157 0.1063 0.1271 REMARK 3 24 1.2872 - 1.2691 1.00 3059 170 0.1084 0.1282 REMARK 3 25 1.2691 - 1.2519 1.00 3075 155 0.1079 0.1340 REMARK 3 26 1.2519 - 1.2356 1.00 3112 138 0.1147 0.1396 REMARK 3 27 1.2356 - 1.2202 1.00 3135 135 0.1127 0.1433 REMARK 3 28 1.2202 - 1.2055 0.99 3042 149 0.1193 0.1656 REMARK 3 29 1.2055 - 1.1915 0.96 2988 154 0.1275 0.1607 REMARK 3 30 1.1915 - 1.1781 0.91 2816 118 0.1432 0.1610 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.017 2030 REMARK 3 ANGLE : 1.734 2734 REMARK 3 CHIRALITY : 0.112 303 REMARK 3 PLANARITY : 0.011 352 REMARK 3 DIHEDRAL : 14.127 767 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JJ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03317 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.178 REMARK 200 RESOLUTION RANGE LOW (A) : 23.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.6000 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: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M SODIUM CITRATE, 0.1M HEPES PH 7.4, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 43.11733 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 86.23467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.23467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.11733 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 400 REMARK 400 COMPOUND REMARK 400 THE 2,6, DIMETHYLBENZOIC ACID FRAGMENT IN RESIDUE 1U8 OF THE REMARK 400 CASPASE INHIBITOR IS REMOVED DURING COVALENT ATTACHMENT TO CASPASE REMARK 400 REMARK 400 THE ACE-1MH-ASP-B3L-HLX-1U8 IS PEPTIDE-LIKE, A MEMBER OF CASPASE REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ACE-1MH-ASP-B3L-HLX-1U8 REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 MET A 216 REMARK 465 SER A 217 REMARK 465 GLU A 218 REMARK 465 SER A 219 REMARK 465 GLN A 220 REMARK 465 THR A 221 REMARK 465 LEU A 222 REMARK 465 SER A 375 REMARK 465 GLU A 376 REMARK 465 GLU A 377 REMARK 465 GLN A 378 REMARK 465 PRO A 379 REMARK 465 TYR A 380 REMARK 465 LEU A 381 REMARK 465 GLU A 382 REMARK 465 MET A 383 REMARK 465 ASP A 384 REMARK 465 LEU A 385 REMARK 465 SER A 386 REMARK 465 SER A 387 REMARK 465 PRO A 388 REMARK 465 GLN A 389 REMARK 465 ASP A 479 REMARK 465 ALA A 480 REMARK 465 ALA A 481 REMARK 465 ALA A 482 REMARK 465 LEU A 483 REMARK 465 GLU A 484 REMARK 465 HIS A 485 REMARK 465 HIS A 486 REMARK 465 HIS A 487 REMARK 465 HIS A 488 REMARK 465 HIS A 489 REMARK 465 HIS A 490 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 LYS A 320 CG CD CE NZ REMARK 470 GLU A 372 CG CD OE1 OE2 REMARK 470 ARG A 391 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 431 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 NZ LYS A 473 O HOH A 996 2.04 REMARK 500 O HOH A 913 O HOH A 1001 2.05 REMARK 500 O HOH A 853 O HOH A 997 2.07 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 411 CB SER A 411 OG -0.111 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 ASP A 319 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 327 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 THR A 467 CA - CB - CG2 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG A 471 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 471 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 B3L B 504 CA - C - N ANGL. DEV. = 16.6 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 MET A 228 69.51 -151.83 REMARK 500 ASN A 408 -11.99 83.60 REMARK 500 B3L B 504 -62.40 -106.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 B3L B 504 HLX B 505 -145.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 413 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 B3L B 504 17.83 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 DTD A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTD A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF CASPASE INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F9E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO REMARK 900 RELATED ID: 1QTN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TETRAPEPTIDE REMARK 900 INHIBITOR ACE-IETD-ALDEHYDE REMARK 900 RELATED ID: 1QDU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-8 WITH THE TRIPEPTIDE REMARK 900 KETONE INHIBITOR ZEVD-DCBMK REMARK 900 RELATED ID: 4JJ8 RELATED DB: PDB REMARK 900 RELATED ID: 4JJE RELATED DB: PDB DBREF 4JJ7 A 217 479 UNP Q14790 CASP8_HUMAN 217 479 DBREF 4JJ7 B 501 506 PDB 4JJ7 4JJ7 501 506 SEQADV 4JJ7 MET A 216 UNP Q14790 INITIATING METHIONINE SEQADV 4JJ7 ALA A 480 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 ALA A 481 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 ALA A 482 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 LEU A 483 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 GLU A 484 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 HIS A 485 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 HIS A 486 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 HIS A 487 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 HIS A 488 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 HIS A 489 UNP Q14790 EXPRESSION TAG SEQADV 4JJ7 HIS A 490 UNP Q14790 EXPRESSION TAG SEQRES 1 A 275 MET SER GLU SER GLN THR LEU ASP LYS VAL TYR GLN MET SEQRES 2 A 275 LYS SER LYS PRO ARG GLY TYR CYS LEU ILE ILE ASN ASN SEQRES 3 A 275 HIS ASN PHE ALA LYS ALA ARG GLU LYS VAL PRO LYS LEU SEQRES 4 A 275 HIS SER ILE ARG ASP ARG ASN GLY THR HIS LEU ASP ALA SEQRES 5 A 275 GLY ALA LEU THR THR THR PHE GLU GLU LEU HIS PHE GLU SEQRES 6 A 275 ILE LYS PRO HIS ASP ASP CYS THR VAL GLU GLN ILE TYR SEQRES 7 A 275 GLU ILE LEU LYS ILE TYR GLN LEU MET ASP HIS SER ASN SEQRES 8 A 275 MET ASP CYS PHE ILE CYS CYS ILE LEU SER HIS GLY ASP SEQRES 9 A 275 LYS GLY ILE ILE TYR GLY THR ASP GLY GLN GLU ALA PRO SEQRES 10 A 275 ILE TYR GLU LEU THR SER GLN PHE THR GLY LEU LYS CYS SEQRES 11 A 275 PRO SER LEU ALA GLY LYS PRO LYS VAL PHE PHE ILE GLN SEQRES 12 A 275 ALA CYS GLN GLY ASP ASN TYR GLN LYS GLY ILE PRO VAL SEQRES 13 A 275 GLU THR ASP SER GLU GLU GLN PRO TYR LEU GLU MET ASP SEQRES 14 A 275 LEU SER SER PRO GLN THR ARG TYR ILE PRO ASP GLU ALA SEQRES 15 A 275 ASP PHE LEU LEU GLY MET ALA THR VAL ASN ASN CYS VAL SEQRES 16 A 275 SER TYR ARG ASN PRO ALA GLU GLY THR TRP TYR ILE GLN SEQRES 17 A 275 SER LEU CYS GLN SER LEU ARG GLU ARG CYS PRO ARG GLY SEQRES 18 A 275 ASP ASP ILE LEU THR ILE LEU THR GLU VAL ASN TYR GLU SEQRES 19 A 275 VAL SER ASN LYS ASP ASP LYS LYS ASN MET GLY LYS GLN SEQRES 20 A 275 MET PRO GLN PRO THR PHE THR LEU ARG LYS LYS LEU VAL SEQRES 21 A 275 PHE PRO SER ASP ALA ALA ALA LEU GLU HIS HIS HIS HIS SEQRES 22 A 275 HIS HIS SEQRES 1 B 6 ACE 1MH ASP B3L HLX 1U8 HET ACE B 501 3 HET 1MH B 502 11 HET B3L B 504 9 HET HLX B 505 9 HET 1U8 B 506 9 HET DTD A 601 8 HET DTD A 602 8 HETNAM ACE ACETYL GROUP HETNAM 1MH 3-PYRIDIN-3-YL-L-ALANINE HETNAM B3L (3S)-3-AMINO-5-METHYLHEXANOIC ACID HETNAM HLX 5-METHYL-L-NORLEUCINE HETNAM 1U8 (3S)-3-AMINO-5-[(2,6-DIMETHYLBENZOYL)OXY]-4- HETNAM 2 1U8 OXOPENTANOIC ACID HETNAM DTD DITHIANE DIOL HETSYN B3L (S)-BETA-3-HOMOLEUCINE FORMUL 2 ACE C2 H4 O FORMUL 2 1MH C8 H10 N2 O2 FORMUL 2 B3L C7 H15 N O2 FORMUL 2 HLX C7 H15 N O2 FORMUL 2 1U8 C14 H17 N O5 FORMUL 3 DTD 2(C4 H8 O2 S2) FORMUL 5 HOH *269(H2 O) HELIX 1 1 PHE A 244 VAL A 251 1 8 HELIX 2 2 PRO A 252 HIS A 255 5 4 HELIX 3 3 GLY A 262 LEU A 277 1 16 HELIX 4 4 THR A 288 MET A 302 1 15 HELIX 5 5 ILE A 333 SER A 338 1 6 HELIX 6 6 GLN A 339 THR A 341 5 3 HELIX 7 7 CYS A 345 ALA A 349 5 5 HELIX 8 8 TRP A 420 CYS A 433 1 14 HELIX 9 9 PRO A 434 GLY A 436 5 3 HELIX 10 10 ASP A 438 SER A 451 1 14 SHEET 1 A 6 GLU A 280 ASP A 285 0 SHEET 2 A 6 TYR A 235 ASN A 240 1 N ASN A 240 O HIS A 284 SHEET 3 A 6 PHE A 310 LEU A 315 1 O CYS A 313 N ILE A 239 SHEET 4 A 6 LYS A 353 GLN A 358 1 O GLN A 358 N ILE A 314 SHEET 5 A 6 PHE A 399 MET A 403 1 O GLY A 402 N PHE A 355 SHEET 6 A 6 GLN A 465 PHE A 468 -1 O THR A 467 N LEU A 401 SHEET 1 B 3 GLY A 318 ASP A 319 0 SHEET 2 B 3 ILE A 322 TYR A 324 -1 O ILE A 322 N ASP A 319 SHEET 3 B 3 GLU A 330 PRO A 332 -1 O ALA A 331 N ILE A 323 SHEET 1 C 2 ARG A 413 ASN A 414 0 SHEET 2 C 2 GLY A 418 THR A 419 -1 O GLY A 418 N ASN A 414 LINK SG CYS A 360 C9 1U8 B 506 1555 1555 1.87 LINK C ACE B 501 N 1MH B 502 1555 1555 1.34 LINK C 1MH B 502 N ASP B 503 1555 1555 1.34 LINK C ASP B 503 N B3L B 504 1555 1555 1.33 LINK C B3L B 504 N HLX B 505 1555 1555 1.31 LINK C HLX B 505 N 1U8 B 506 1555 1555 1.32 CISPEP 1 LYS A 231 PRO A 232 0 5.71 SITE 1 AC1 3 TYR A 392 ASP A 454 MET A 459 SITE 1 AC2 10 TYR A 334 THR A 337 GLU A 396 PHE A 399 SITE 2 AC2 10 LEU A 401 THR A 469 HOH A 874 HOH A 876 SITE 3 AC2 10 HOH A 913 HOH A1001 SITE 1 AC3 24 ARG A 258 ARG A 260 ASN A 261 SER A 316 SITE 2 AC3 24 HIS A 317 GLY A 318 GLN A 358 CYS A 360 SITE 3 AC3 24 SER A 411 TYR A 412 ARG A 413 PRO A 415 SITE 4 AC3 24 HOH B 601 HOH B 602 HOH B 603 HOH B 604 SITE 5 AC3 24 HOH B 605 HOH B 607 HOH B 608 HOH B 609 SITE 6 AC3 24 HOH B 611 HOH B 613 HOH B 614 HOH B 615 CRYST1 62.844 62.844 129.352 90.00 90.00 120.00 P 31 2 1 6 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 0.015912 0.009187 0.000000 0.00000 SCALE2 0.000000 0.018374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007731 0.00000