PDB Short entry for 3R7S HEADER HYDROLASE 22-MAR-11 3R7S TITLE CRYSTAL STRUCTURE OF APO CASPASE2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-2 SUBUNIT P18; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 175-333; COMPND 5 EC: 3.4.22.55; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CASPASE-2 SUBUNIT P12; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: UNP RESIDUES 349-452; COMPND 11 EC: 3.4.22.55; 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 GENE: CASP2, ICH1, NEDD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CASP2, ICH1, NEDD2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR Y.TANG,J.WELLS,M.ARKIN REVDAT 3 17-JUL-19 3R7S 1 REMARK REVDAT 2 19-OCT-11 3R7S 1 JRNL REVDAT 1 27-JUL-11 3R7S 0 JRNL AUTH Y.TANG,J.A.WELLS,M.R.ARKIN JRNL TITL STRUCTURAL AND ENZYMATIC INSIGHTS INTO CASPASE-2 PROTEIN JRNL TITL 2 SUBSTRATE RECOGNITION AND CATALYSIS. JRNL REF J.BIOL.CHEM. V. 286 34147 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21828056 JRNL DOI 10.1074/JBC.M111.247627 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.4_49 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 31691 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1907 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 49.5584 - 5.4266 0.99 2382 154 0.1735 0.2021 REMARK 3 2 5.4266 - 4.3081 1.00 2279 146 0.1287 0.1752 REMARK 3 3 4.3081 - 3.7637 1.00 2242 143 0.1420 0.1786 REMARK 3 4 3.7637 - 3.4197 0.99 2257 144 0.1633 0.2044 REMARK 3 5 3.4197 - 3.1746 0.99 2204 141 0.1889 0.2464 REMARK 3 6 3.1746 - 2.9875 0.98 2176 139 0.2007 0.2629 REMARK 3 7 2.9875 - 2.8379 0.97 2150 140 0.2005 0.2706 REMARK 3 8 2.8379 - 2.7143 0.96 2129 137 0.2044 0.2570 REMARK 3 9 2.7143 - 2.6099 0.95 2105 135 0.2041 0.2470 REMARK 3 10 2.6099 - 2.5198 0.93 2053 134 0.1927 0.2616 REMARK 3 11 2.5198 - 2.4410 0.91 2004 127 0.1885 0.2817 REMARK 3 12 2.4410 - 2.3712 0.91 2006 126 0.1957 0.3072 REMARK 3 13 2.3712 - 2.3088 0.88 1944 126 0.2045 0.2842 REMARK 3 14 2.3088 - 2.2520 0.84 1853 115 0.2113 0.2984 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 : 0.33 REMARK 3 B_SOL : 37.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.15790 REMARK 3 B22 (A**2) : 0.72780 REMARK 3 B33 (A**2) : -13.88570 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 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 : 0.022 4095 REMARK 3 ANGLE : 2.040 5538 REMARK 3 CHIRALITY : 0.139 609 REMARK 3 PLANARITY : 0.010 723 REMARK 3 DIHEDRAL : 20.195 1498 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3R7S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064596. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33253 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 15% PEG 3350, 3MM DTT, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 37.08200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.00100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.40400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.00100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.08200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.40400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 KCAL/MOL 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 ASP A 333 REMARK 465 GLY B 349 REMARK 465 LYS B 350 REMARK 465 GLU B 351 REMARK 465 LYS B 352 REMARK 465 LEU B 353 REMARK 465 THR B 452 REMARK 465 LEU B 453 REMARK 465 GLU B 454 REMARK 465 HIS B 455 REMARK 465 HIS B 456 REMARK 465 HIS B 457 REMARK 465 HIS B 458 REMARK 465 HIS B 459 REMARK 465 HIS B 460 REMARK 465 ASP C 333 REMARK 465 GLY D 349 REMARK 465 LYS D 350 REMARK 465 GLU D 351 REMARK 465 LYS D 352 REMARK 465 LEU D 353 REMARK 465 PRO D 354 REMARK 465 LYS D 355 REMARK 465 MET D 356 REMARK 465 THR D 452 REMARK 465 LEU D 453 REMARK 465 GLU D 454 REMARK 465 HIS D 455 REMARK 465 HIS D 456 REMARK 465 HIS D 457 REMARK 465 HIS D 458 REMARK 465 HIS D 459 REMARK 465 HIS D 460 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 GLU A 213 CG CD OE1 OE2 REMARK 470 GLU A 215 CG CD OE1 OE2 REMARK 470 GLU A 217 CG CD OE1 OE2 REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 GLU A 324 CG CD OE1 OE2 REMARK 470 ARG A 327 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 381 CG CD CE NZ REMARK 470 TYR B 420 OH REMARK 470 THR B 424 OG1 CG2 REMARK 470 GLU B 425 CG CD OE1 OE2 REMARK 470 PHE B 426 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU C 213 CG CD OE1 OE2 REMARK 470 ASP C 223 CG OD1 OD2 REMARK 470 GLU C 253 CG CD OE1 OE2 REMARK 470 GLU C 295 CG CD OE1 OE2 REMARK 470 GLU C 324 CG CD OE1 OE2 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 ASP A 239 CG REMARK 480 GLN A 294 CD REMARK 480 GLN C 189 CD 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 CB CYS C 179 O HOH C 534 2.11 REMARK 500 NH2 ARG C 219 O HOH C 529 2.19 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 OH TYR D 420 O HOH C 513 4455 2.09 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 TYR B 444 CD1 TYR B 444 CE1 0.094 REMARK 500 GLU D 431 CG GLU D 431 CD 0.098 REMARK 500 CYS D 436 CB CYS D 436 SG -0.100 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 301 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG C 219 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG C 265 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 PRO D 451 C - N - CA ANGL. DEV. = 12.8 DEGREES REMARK 500 PRO D 451 C - N - CD ANGL. DEV. = -13.6 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 GLU A 213 13.56 -44.78 REMARK 500 LYS A 214 135.47 -176.40 REMARK 500 GLU A 215 -41.15 49.35 REMARK 500 ASP A 245 66.94 36.71 REMARK 500 SER A 276 -168.38 -164.71 REMARK 500 GLU B 425 108.94 -49.45 REMARK 500 PHE B 426 8.10 144.29 REMARK 500 LEU C 190 41.89 -105.45 REMARK 500 LYS C 214 18.11 167.36 REMARK 500 GLU C 215 46.74 74.48 REMARK 500 LYS D 372 125.63 -37.79 REMARK 500 ALA D 421 83.12 -161.92 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 THR A 211 GLY A 212 -40.82 REMARK 500 LYS A 214 GLU A 215 144.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R7N RELATED DB: PDB REMARK 900 CASPASE-2 BOUND WITH TWO COPIES OF AC-DVAD-CHO REMARK 900 RELATED ID: 3R7B RELATED DB: PDB REMARK 900 CASPASE-2 BOUND TO ONE COPY OF AC-DVAD-CHO REMARK 900 RELATED ID: 3R6L RELATED DB: PDB REMARK 900 CASPASE-2 T380A BOUND WITH AC-VDVAD-CHO REMARK 900 RELATED ID: 3R6G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVE CASPASE-2 BOUND WITH AC-VDVAD-CHO REMARK 900 RELATED ID: 3R5J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVE CASPASE-2 BOUND WITH AC-ADVAD-CHO DBREF 3R7S A 175 333 UNP P42575 CASP2_HUMAN 175 333 DBREF 3R7S B 349 452 UNP P42575 CASP2_HUMAN 349 452 DBREF 3R7S C 175 333 UNP P42575 CASP2_HUMAN 175 333 DBREF 3R7S D 349 452 UNP P42575 CASP2_HUMAN 349 452 SEQADV 3R7S MET A 174 UNP P42575 EXPRESSION TAG SEQADV 3R7S LEU B 453 UNP P42575 EXPRESSION TAG SEQADV 3R7S GLU B 454 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS B 455 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS B 456 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS B 457 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS B 458 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS B 459 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS B 460 UNP P42575 EXPRESSION TAG SEQADV 3R7S MET C 174 UNP P42575 EXPRESSION TAG SEQADV 3R7S LEU D 453 UNP P42575 EXPRESSION TAG SEQADV 3R7S GLU D 454 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS D 455 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS D 456 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS D 457 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS D 458 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS D 459 UNP P42575 EXPRESSION TAG SEQADV 3R7S HIS D 460 UNP P42575 EXPRESSION TAG SEQRES 1 A 160 MET GLN VAL LYS PRO CYS THR PRO GLU PHE TYR GLN THR SEQRES 2 A 160 HIS PHE GLN LEU ALA TYR ARG LEU GLN SER ARG PRO ARG SEQRES 3 A 160 GLY LEU ALA LEU VAL LEU SER ASN VAL HIS PHE THR GLY SEQRES 4 A 160 GLU LYS GLU LEU GLU PHE ARG SER GLY GLY ASP VAL ASP SEQRES 5 A 160 HIS SER THR LEU VAL THR LEU PHE LYS LEU LEU GLY TYR SEQRES 6 A 160 ASP VAL HIS VAL LEU CYS ASP GLN THR ALA GLN GLU MET SEQRES 7 A 160 GLN GLU LYS LEU GLN ASN PHE ALA GLN LEU PRO ALA HIS SEQRES 8 A 160 ARG VAL THR ASP SER CYS ILE VAL ALA LEU LEU SER HIS SEQRES 9 A 160 GLY VAL GLU GLY ALA ILE TYR GLY VAL ASP GLY LYS LEU SEQRES 10 A 160 LEU GLN LEU GLN GLU VAL PHE GLN LEU PHE ASP ASN ALA SEQRES 11 A 160 ASN CYS PRO SER LEU GLN ASN LYS PRO LYS MET PHE PHE SEQRES 12 A 160 ILE GLN ALA CYS ARG GLY ASP GLU THR ASP ARG GLY VAL SEQRES 13 A 160 ASP GLN GLN ASP SEQRES 1 B 112 GLY LYS GLU LYS LEU PRO LYS MET ARG LEU PRO THR ARG SEQRES 2 B 112 SER ASP MET ILE CYS GLY TYR ALA CYS LEU LYS GLY THR SEQRES 3 B 112 ALA ALA MET ARG ASN THR LYS ARG GLY SER TRP TYR ILE SEQRES 4 B 112 GLU ALA LEU ALA GLN VAL PHE SER GLU ARG ALA CYS ASP SEQRES 5 B 112 MET HIS VAL ALA ASP MET LEU VAL LYS VAL ASN ALA LEU SEQRES 6 B 112 ILE LYS ASP ARG GLU GLY TYR ALA PRO GLY THR GLU PHE SEQRES 7 B 112 HIS ARG CYS LYS GLU MET SER GLU TYR CYS SER THR LEU SEQRES 8 B 112 CYS ARG HIS LEU TYR LEU PHE PRO GLY HIS PRO PRO THR SEQRES 9 B 112 LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 160 MET GLN VAL LYS PRO CYS THR PRO GLU PHE TYR GLN THR SEQRES 2 C 160 HIS PHE GLN LEU ALA TYR ARG LEU GLN SER ARG PRO ARG SEQRES 3 C 160 GLY LEU ALA LEU VAL LEU SER ASN VAL HIS PHE THR GLY SEQRES 4 C 160 GLU LYS GLU LEU GLU PHE ARG SER GLY GLY ASP VAL ASP SEQRES 5 C 160 HIS SER THR LEU VAL THR LEU PHE LYS LEU LEU GLY TYR SEQRES 6 C 160 ASP VAL HIS VAL LEU CYS ASP GLN THR ALA GLN GLU MET SEQRES 7 C 160 GLN GLU LYS LEU GLN ASN PHE ALA GLN LEU PRO ALA HIS SEQRES 8 C 160 ARG VAL THR ASP SER CYS ILE VAL ALA LEU LEU SER HIS SEQRES 9 C 160 GLY VAL GLU GLY ALA ILE TYR GLY VAL ASP GLY LYS LEU SEQRES 10 C 160 LEU GLN LEU GLN GLU VAL PHE GLN LEU PHE ASP ASN ALA SEQRES 11 C 160 ASN CYS PRO SER LEU GLN ASN LYS PRO LYS MET PHE PHE SEQRES 12 C 160 ILE GLN ALA CYS ARG GLY ASP GLU THR ASP ARG GLY VAL SEQRES 13 C 160 ASP GLN GLN ASP SEQRES 1 D 112 GLY LYS GLU LYS LEU PRO LYS MET ARG LEU PRO THR ARG SEQRES 2 D 112 SER ASP MET ILE CYS GLY TYR ALA CYS LEU LYS GLY THR SEQRES 3 D 112 ALA ALA MET ARG ASN THR LYS ARG GLY SER TRP TYR ILE SEQRES 4 D 112 GLU ALA LEU ALA GLN VAL PHE SER GLU ARG ALA CYS ASP SEQRES 5 D 112 MET HIS VAL ALA ASP MET LEU VAL LYS VAL ASN ALA LEU SEQRES 6 D 112 ILE LYS ASP ARG GLU GLY TYR ALA PRO GLY THR GLU PHE SEQRES 7 D 112 HIS ARG CYS LYS GLU MET SER GLU TYR CYS SER THR LEU SEQRES 8 D 112 CYS ARG HIS LEU TYR LEU PHE PRO GLY HIS PRO PRO THR SEQRES 9 D 112 LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 5 HOH *135(H2 O) HELIX 1 1 THR A 180 PHE A 188 1 9 HELIX 2 2 GLN A 189 ALA A 191 5 3 HELIX 3 3 GLY A 221 LEU A 236 1 16 HELIX 4 4 THR A 247 LEU A 261 1 15 HELIX 5 5 PRO A 262 THR A 267 5 6 HELIX 6 6 LEU A 293 PHE A 300 1 8 HELIX 7 7 CYS A 305 GLN A 309 5 5 HELIX 8 8 TRP B 385 ALA B 398 1 14 HELIX 9 9 HIS B 402 ARG B 417 1 16 HELIX 10 10 THR C 180 PHE C 188 1 9 HELIX 11 11 GLN C 189 ALA C 191 5 3 HELIX 12 12 GLY C 221 LEU C 236 1 16 HELIX 13 13 THR C 247 GLN C 260 1 14 HELIX 14 14 LEU C 261 VAL C 266 5 6 HELIX 15 15 LEU C 293 PHE C 300 1 8 HELIX 16 16 CYS C 305 GLN C 309 5 5 HELIX 17 17 TRP D 385 ALA D 398 1 14 HELIX 18 18 HIS D 402 ARG D 417 1 16 SHEET 1 A12 TYR A 238 CYS A 244 0 SHEET 2 A12 GLY A 200 SER A 206 1 N ALA A 202 O HIS A 241 SHEET 3 A12 SER A 269 LEU A 275 1 O ALA A 273 N LEU A 203 SHEET 4 A12 LYS A 313 GLN A 318 1 O MET A 314 N CYS A 270 SHEET 5 A12 MET B 364 TYR B 368 1 O GLY B 367 N ILE A 317 SHEET 6 A12 GLU B 434 SER B 437 -1 O GLU B 434 N TYR B 368 SHEET 7 A12 GLU D 434 SER D 437 -1 O TYR D 435 N SER B 437 SHEET 8 A12 MET D 364 TYR D 368 -1 N CYS D 366 O CYS D 436 SHEET 9 A12 LYS C 313 GLN C 318 1 N PHE C 315 O GLY D 367 SHEET 10 A12 SER C 269 LEU C 275 1 N CYS C 270 O MET C 314 SHEET 11 A12 GLY C 200 SER C 206 1 N LEU C 203 O ALA C 273 SHEET 12 A12 ASP C 239 CYS C 244 1 O HIS C 241 N ALA C 202 SHEET 1 B 3 GLY A 278 VAL A 279 0 SHEET 2 B 3 ALA A 282 TYR A 284 -1 O ALA A 282 N VAL A 279 SHEET 3 B 3 LEU A 290 GLN A 292 -1 O LEU A 291 N ILE A 283 SHEET 1 C 2 ARG B 357 LEU B 358 0 SHEET 2 C 2 VAL C 329 ASP C 330 -1 O VAL C 329 N LEU B 358 SHEET 1 D 2 ARG B 378 ASN B 379 0 SHEET 2 D 2 GLY B 383 SER B 384 -1 O GLY B 383 N ASN B 379 SHEET 1 E 3 GLY C 278 VAL C 279 0 SHEET 2 E 3 ALA C 282 TYR C 284 -1 O ALA C 282 N VAL C 279 SHEET 3 E 3 LEU C 290 GLN C 292 -1 O LEU C 291 N ILE C 283 SHEET 1 F 2 ARG D 378 ASN D 379 0 SHEET 2 F 2 GLY D 383 SER D 384 -1 O GLY D 383 N ASN D 379 SSBOND 1 CYS B 436 CYS D 436 1555 1555 2.18 CISPEP 1 ARG A 197 PRO A 198 0 1.83 CISPEP 2 HIS B 449 PRO B 450 0 -5.73 CISPEP 3 ARG C 197 PRO C 198 0 -3.01 CISPEP 4 HIS D 449 PRO D 450 0 7.43 CRYST1 74.164 82.808 112.002 90.00 90.00 90.00 P 21 21 21 8 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 0.013484 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012076 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008928 0.00000