PDB Short entry for 3R5J HEADER HYDROLASE/HYDROLASE INHIBITOR 18-MAR-11 3R5J TITLE CRYSTAL STRUCTURE OF ACTIVE CASPASE-2 BOUND WITH AC-ADVAD-CHO COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-2 SUBUNIT P18; COMPND 3 CHAIN: A, C; COMPND 4 EC: 3.4.22.55; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CASPASE-2 SUBUNIT P12; COMPND 8 CHAIN: B, D; COMPND 9 EC: 3.4.22.55; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PEPTIDE INHIBITOR (ACE)ADVAD-CHO; COMPND 13 CHAIN: F, E; COMPND 14 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; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES KEYWDS HYDROLASE, APOPTOSIS, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.TANG,J.WELLS,M.ARKIN REVDAT 2 19-OCT-11 3R5J 1 JRNL REVDAT 1 27-JUL-11 3R5J 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. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 56115 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2982 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4025 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 209 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3990 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 325 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54000 REMARK 3 B22 (A**2) : -0.99000 REMARK 3 B33 (A**2) : -0.55000 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : -0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.112 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.066 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4134 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5603 ; 1.372 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 531 ; 5.572 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;33.951 ;23.656 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 688 ;13.020 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;12.733 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 622 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3140 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2606 ; 0.908 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4168 ; 1.715 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1528 ; 2.498 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1424 ; 4.037 ; 4.500 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3R5J 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 RCSB ID CODE IS RCSB064515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-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 : 59418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 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) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 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 (%): 48.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 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 31.65050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.07450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.50350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.07450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.65050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.50350 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, F 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: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, F, E 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 THERE ARE NO LINKS BETWEEN CYS 320 AND CHAINS E,F 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 THR A 211 REMARK 465 GLY A 212 REMARK 465 GLU A 213 REMARK 465 LYS A 214 REMARK 465 GLU A 215 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 PRO B 354 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 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 GLN A 175 CG CD OE1 NE2 REMARK 470 LYS A 177 CD CE NZ REMARK 470 GLU A 182 CG CD OE1 OE2 REMARK 470 GLN A 189 CD OE1 NE2 REMARK 470 ARG A 193 CZ NH1 NH2 REMARK 470 ARG A 197 CZ NH1 NH2 REMARK 470 GLU A 217 CG CD OE1 OE2 REMARK 470 GLU A 295 CG CD OE1 OE2 REMARK 470 ASP A 323 CG OD1 OD2 REMARK 470 GLU A 324 CG CD OE1 OE2 REMARK 470 THR A 325 OG1 CG2 REMARK 470 LYS B 355 CG CD CE NZ REMARK 470 LYS B 372 CG CD CE NZ REMARK 470 LYS B 381 CG CD CE NZ REMARK 470 GLN B 392 CD OE1 NE2 REMARK 470 GLU B 425 CG CD OE1 OE2 REMARK 470 GLN C 175 CG CD OE1 NE2 REMARK 470 LYS C 177 CG CD CE NZ REMARK 470 GLU C 182 CG CD OE1 OE2 REMARK 470 LEU C 190 CD1 REMARK 470 ARG C 193 CZ NH1 NH2 REMARK 470 GLU C 213 CG CD OE1 OE2 REMARK 470 GLU C 217 CD OE1 OE2 REMARK 470 GLU C 253 CD OE1 OE2 REMARK 470 ARG C 265 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 324 CG CD OE1 OE2 REMARK 470 ARG C 327 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 396 CD OE1 OE2 REMARK 470 GLU D 425 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 MET B 401 CG SD CE REMARK 480 MET D 401 CE 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 O HOH B 553 O HOH D 563 2.08 REMARK 500 O LEU A 190 O HOH A 590 2.08 REMARK 500 SG CYS D 366 O HOH D 562 2.14 REMARK 500 O HOH A 556 O HOH A 593 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 194 71.68 -151.20 REMARK 500 ASP B 400 13.86 -143.83 REMARK 500 ALA B 421 61.97 -159.76 REMARK 500 ARG B 428 17.23 59.40 REMARK 500 LEU C 194 74.35 -154.10 REMARK 500 ASP D 400 11.38 -144.70 REMARK 500 ALA D 421 57.10 -166.28 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 CHAIN E OF PEPTIDE (ACE)ADVAD- REMARK 800 CHO REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN F OF PEPTIDE (ACE)ADVAD- REMARK 800 CHO 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- REMARK 900 CHO REMARK 900 RELATED ID: 3R7S RELATED DB: PDB REMARK 900 CRYSTAL CTRUCTURE OF APO CASPASE2 DBREF 3R5J A 175 329 UNP P42575 CASP2_HUMAN 175 333 DBREF 3R5J B 349 452 UNP P42575 CASP2_HUMAN 349 452 DBREF 3R5J C 175 333 UNP P42575 CASP2_HUMAN 175 333 DBREF 3R5J D 349 452 UNP P42575 CASP2_HUMAN 349 452 DBREF 3R5J F 401 406 PDB 3R5J 3R5J 401 406 DBREF 3R5J E 401 406 PDB 3R5J 3R5J 401 406 SEQADV 3R5J MET A 174 UNP P42575 EXPRESSION TAG SEQADV 3R5J LEU B 453 UNP P42575 EXPRESSION TAG SEQADV 3R5J GLU B 454 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS B 455 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS B 456 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS B 457 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS B 458 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS B 459 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS B 460 UNP P42575 EXPRESSION TAG SEQADV 3R5J MET C 174 UNP P42575 EXPRESSION TAG SEQADV 3R5J LEU D 453 UNP P42575 EXPRESSION TAG SEQADV 3R5J GLU D 454 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS D 455 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS D 456 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS D 457 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS D 458 UNP P42575 EXPRESSION TAG SEQADV 3R5J HIS D 459 UNP P42575 EXPRESSION TAG SEQADV 3R5J 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 SEQRES 1 F 6 ACE ALA ASP VAL ALA ASA SEQRES 1 E 6 ACE ALA ASP VAL ALA ASA MODRES 3R5J ASA F 406 ASP ASPARTIC ALDEHYDE MODRES 3R5J ASA E 406 ASP ASPARTIC ALDEHYDE HET ACE F 401 3 HET ASA F 406 8 HET ACE E 401 3 HET ASA E 406 8 HETNAM ACE ACETYL GROUP HETNAM ASA ASPARTIC ALDEHYDE FORMUL 5 ACE 2(C2 H4 O) FORMUL 5 ASA 2(C4 H7 N O3) FORMUL 7 HOH *325(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 GLN A 260 1 14 HELIX 5 5 LEU A 261 VAL A 266 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 THR C 267 5 7 HELIX 15 15 LEU C 293 LEU C 299 1 7 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 ASP A 239 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 GLN A 318 N LEU A 274 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 TYR D 368 O GLU D 434 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 VAL A 329 ASP A 330 0 SHEET 2 C 2 ARG D 357 LEU D 358 -1 O LEU D 358 N VAL A 329 SHEET 1 D 2 ARG B 357 LEU B 358 0 SHEET 2 D 2 VAL C 329 ASP C 330 -1 O VAL C 329 N LEU B 358 SHEET 1 E 3 GLY B 383 SER B 384 0 SHEET 2 E 3 MET B 377 ASN B 379 -1 N ASN B 379 O GLY B 383 SHEET 3 E 3 ASP E 403 ALA E 405 -1 O VAL E 404 N ARG B 378 SHEET 1 F 3 GLY C 278 VAL C 279 0 SHEET 2 F 3 ALA C 282 TYR C 284 -1 O ALA C 282 N VAL C 279 SHEET 3 F 3 LEU C 290 GLN C 292 -1 O LEU C 291 N ILE C 283 SHEET 1 G 3 GLY D 383 SER D 384 0 SHEET 2 G 3 MET D 377 ASN D 379 -1 N ASN D 379 O GLY D 383 SHEET 3 G 3 ASP F 403 ALA F 405 -1 O VAL F 404 N ARG D 378 SSBOND 1 CYS B 436 CYS D 436 1555 1555 2.12 LINK C ACE F 401 N ALA F 402 1555 1555 1.33 LINK C ALA F 405 N ASA F 406 1555 1555 1.33 LINK C ACE E 401 N ALA E 402 1555 1555 1.33 LINK C ALA E 405 N ASA E 406 1555 1555 1.33 CISPEP 1 ARG A 197 PRO A 198 0 -0.67 CISPEP 2 HIS B 449 PRO B 450 0 -0.95 CISPEP 3 ARG C 197 PRO C 198 0 -1.38 CISPEP 4 HIS D 449 PRO D 450 0 2.27 SITE 1 AC1 15 ARG A 219 HIS A 277 GLY A 278 GLN A 318 SITE 2 AC1 15 CYS A 320 ALA B 376 MET B 377 ARG B 378 SITE 3 AC1 15 ASN B 379 THR B 380 TRP B 385 GLY B 419 SITE 4 AC1 15 TYR B 420 ALA B 421 PHE B 426 SITE 1 AC2 17 ASP B 416 ARG C 219 HIS C 277 GLY C 278 SITE 2 AC2 17 GLN C 318 CYS C 320 ALA D 376 MET D 377 SITE 3 AC2 17 ARG D 378 ASN D 379 THR D 380 LYS D 381 SITE 4 AC2 17 TRP D 385 GLY D 419 TYR D 420 ALA D 421 SITE 5 AC2 17 PHE D 426 CRYST1 63.301 97.007 98.149 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 0.015798 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010189 0.00000