PDB Short entry for 2DKO HEADER HYDROLASE/HYDROLASE INHIBITOR 12-APR-06 2DKO TITLE EXTENDED SUBSTRATE RECOGNITION IN CASPASE-3 REVEALED BY HIGH TITLE 2 RESOLUTION X-RAY STRUCTURE ANALYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CASPASE-3 P17 SUBUNIT, RESIDUES 29-174; COMPND 5 EC: 3.4.22.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CASPASE-3; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: CASPASE-3 P12 SUBUNIT, RESIDUES 175-277; COMPND 11 EC: 3.4.22.-; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: PHQ-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE; COMPND 16 CHAIN: I; COMPND 17 SYNONYM: Z-DEVD-CMK; COMPND 18 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11D; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET11D; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS LOW BARRIER HYDROGEN BOND, CASPASE, DRUG DESIGN, RADIATION DAMAGE, KEYWDS 2 TETRAHEDRAL INTERMEDIATE, PROTEASE, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.R.E.MITTL,R.GANESAN,S.JELAKOVIC,M.G.GRUTTER REVDAT 4 02-APR-14 2DKO 1 ATOM SEQRES REVDAT 3 13-JUL-11 2DKO 1 VERSN REVDAT 2 24-FEB-09 2DKO 1 VERSN REVDAT 1 04-JUL-06 2DKO 0 JRNL AUTH R.GANESAN,P.R.E.MITTL,S.JELAKOVIC,M.G.GRUTTER JRNL TITL EXTENDED SUBSTRATE RECOGNITION IN CASPASE-3 REVEALED BY HIGH JRNL TITL 2 RESOLUTION X-RAY STRUCTURE ANALYSIS JRNL REF J.MOL.BIOL. V. 359 1378 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16787777 JRNL DOI 10.1016/J.JMB.2006.04.051 REMARK 2 REMARK 2 RESOLUTION. 1.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.142 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 1.800 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2049 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 113110 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.108 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 1.900 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1255 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 65131 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2029 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 335 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2362.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1933.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 20 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 20202 REMARK 3 NUMBER OF RESTRAINTS : 24660 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.035 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.086 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.113 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.044 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.054 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-APR-06. REMARK 100 THE RCSB ID CODE IS RCSB025528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8498 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 113110 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.060 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.060 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1CP3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.75, VAPOR DIFFUSION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 33.82500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.94500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.08000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.82500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.94500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.08000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.82500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.94500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.08000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.82500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.94500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.08000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 16910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, I 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 BIOMT1 2 -1.000000 0.000000 0.000000 67.65000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 96.16000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 392 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THE UNBOUND INHIBITOR (CHAIN I) IS CARBOBENZOXY-ASP-GLU-VAL-ASP- REMARK 400 CHLOROMETHYLKETONE. UPON REACTION WITH THE ENZYME CHLORINE REMARK 400 DISSOCIATES AND THE INHIBITOR COVALENTLY BINDS TO THE SG CYS 163 A REMARK 400 OF THE ENZYME FORMING A TETRAHEDRAL INTERMEDIATE. REMARK 400 REMARK 400 THE N-[(BENZYLOXY)CARBONYL]-L-ALPHA-ASPARTYL-L-ALPHA-GLUTAMYL-N- REMARK 400 [(1S)-1-(CARBOXYMETHYL)-3-CHLORO-2-OXOPROPYL]-L-VALINAMIDE IS REMARK 400 PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: N-[(BENZYLOXY)CARBONYL]-L-ALPHA-ASPARTYL-L-ALPHA-GLUTAMYL-N REMARK 400 -[(1S)-1-(CARBOXYMETHYL)-3-CHLORO-2-OXOPROPYL]-L-VALINAMIDE REMARK 400 CHAIN: I 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 PHQ I 1 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 40 CB - CG - OD2 ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG A 75 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 86 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 101 CD - NE - CZ ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 147 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 HIS B 185 CA - CB - CG ANGL. DEV. = 20.9 DEGREES REMARK 500 LEU B 194 CA - CB - CG ANGL. DEV. = 15.9 DEGREES REMARK 500 TYR B 195 CG - CD2 - CE2 ANGL. DEV. = -4.8 DEGREES REMARK 500 TYR B 197 CG - CD2 - CE2 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 207 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 GLN B 217 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 ASP B 228 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 MET B 233 CG - SD - CE ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG B 238 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG B 241 NE - CZ - NH1 ANGL. DEV. = 3.0 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 ARG A 64 68.80 -100.76 REMARK 500 LYS B 229 -28.74 -140.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 248 DISTANCE = 5.64 ANGSTROMS REMARK 525 HOH A 252 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH B 374 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH B 381 DISTANCE = 5.50 ANGSTROMS REMARK 525 HOH B 382 DISTANCE = 5.25 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF PHQ-ASP-GLU-VAL-ASP- REMARK 800 CHLOROMETHYLKETONE DBREF 2DKO A 29 174 UNP P42574 CASP3_HUMAN 29 174 DBREF 2DKO B 175 277 UNP P42574 CASP3_HUMAN 175 277 DBREF 2DKO I 1 6 PDB 2DKO 2DKO 1 6 SEQADV 2DKO ALA B 175 UNP P42574 ASP 175 ENGINEERED MUTATION SEQRES 1 A 146 SER GLY ILE SER LEU ASP ASN SER TYR LYS MET ASP TYR SEQRES 2 A 146 PRO GLU MET GLY LEU CYS ILE ILE ILE ASN ASN LYS ASN SEQRES 3 A 146 PHE HIS LYS SER THR GLY MET THR SER ARG SER GLY THR SEQRES 4 A 146 ASP VAL ASP ALA ALA ASN LEU ARG GLU THR PHE ARG ASN SEQRES 5 A 146 LEU LYS TYR GLU VAL ARG ASN LYS ASN ASP LEU THR ARG SEQRES 6 A 146 GLU GLU ILE VAL GLU LEU MET ARG ASP VAL SER LYS GLU SEQRES 7 A 146 ASP HIS SER LYS ARG SER SER PHE VAL CYS VAL LEU LEU SEQRES 8 A 146 SER HIS GLY GLU GLU GLY ILE ILE PHE GLY THR ASN GLY SEQRES 9 A 146 PRO VAL ASP LEU LYS LYS ILE THR ASN PHE PHE ARG GLY SEQRES 10 A 146 ASP ARG CYS ARG SER LEU THR GLY LYS PRO LYS LEU PHE SEQRES 11 A 146 ILE ILE GLN ALA CYS ARG GLY THR GLU LEU ASP CYS GLY SEQRES 12 A 146 ILE GLU THR SEQRES 1 B 103 ALA SER GLY VAL ASP ASP ASP MET ALA CYS HIS LYS ILE SEQRES 2 B 103 PRO VAL GLU ALA ASP PHE LEU TYR ALA TYR SER THR ALA SEQRES 3 B 103 PRO GLY TYR TYR SER TRP ARG ASN SER LYS ASP GLY SER SEQRES 4 B 103 TRP PHE ILE GLN SER LEU CYS ALA MET LEU LYS GLN TYR SEQRES 5 B 103 ALA ASP LYS LEU GLU PHE MET HIS ILE LEU THR ARG VAL SEQRES 6 B 103 ASN ARG LYS VAL ALA THR GLU PHE GLU SER PHE SER PHE SEQRES 7 B 103 ASP ALA THR PHE HIS ALA LYS LYS GLN ILE PRO CYS ILE SEQRES 8 B 103 VAL SER MET LEU THR LYS GLU LEU TYR PHE TYR HIS SEQRES 1 I 6 PHQ ASP GLU VAL ASP 0QE HET 0QE I 6 1 HETNAM 0QE CHLOROMETHANE HETSYN 0QE CHLORO METHYL GROUP FORMUL 3 0QE C H3 CL FORMUL 4 HOH *335(H2 O) HELIX 1 1 HIS A 56 GLY A 60 5 5 HELIX 2 2 GLY A 66 LEU A 81 1 16 HELIX 3 3 THR A 92 GLU A 106 1 15 HELIX 4 4 LEU A 136 PHE A 142 1 7 HELIX 5 5 CYS A 148 THR A 152 5 5 HELIX 6 6 TRP B 214 ALA B 227 1 14 HELIX 7 7 GLU B 231 PHE B 247 1 17 HELIX 8 8 ASP B 253 HIS B 257 5 5 SHEET 1 A 6 GLU A 84 ASN A 89 0 SHEET 2 A 6 GLU A 43 ASN A 51 1 N ASN A 51 O LYS A 88 SHEET 3 A 6 ARG A 111 LEU A 119 1 O VAL A 117 N ILE A 48 SHEET 4 A 6 LYS A 156 GLN A 161 1 O LEU A 157 N PHE A 114 SHEET 5 A 6 PHE B 193 TYR B 197 1 O LEU B 194 N PHE A 158 SHEET 6 A 6 CYS B 264 SER B 267 -1 O VAL B 266 N TYR B 195 SHEET 1 B 3 GLY A 122 GLU A 123 0 SHEET 2 B 3 ILE A 126 GLY A 129 -1 O ILE A 126 N GLU A 123 SHEET 3 B 3 GLY A 132 ASP A 135 -1 O GLY A 132 N GLY A 129 SHEET 1 C 3 GLY B 212 SER B 213 0 SHEET 2 C 3 TRP B 206 ASN B 208 -1 N ASN B 208 O GLY B 212 SHEET 3 C 3 GLU I 3 VAL I 4 -1 O GLU I 3 N ARG B 207 LINK C ASP I 5 C1 0QE I 6 1555 1555 1.59 LINK SG CYS A 163 C ASP I 5 1555 1555 2.03 SITE 1 AC1 24 SER A 58 ARG A 64 SER A 65 HIS A 121 SITE 2 AC1 24 GLY A 122 GLN A 161 CYS A 163 HOH A 196 SITE 3 AC1 24 HOH A 391 ASP B 179 TYR B 204 SER B 205 SITE 4 AC1 24 TRP B 206 ARG B 207 ASN B 208 TRP B 214 SITE 5 AC1 24 SER B 249 PHE B 250 HOH B 310 HOH B 343 SITE 6 AC1 24 HOH I 181 HOH I 203 HOH I 236 HOH I 238 CRYST1 67.650 83.890 96.160 90.00 90.00 90.00 I 2 2 2 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 0.014782 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011920 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010399 0.00000