HEADER HYDROLASE 23-MAY-00 1F2B TITLE CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO VINYL TITLE 2 SULFONE DERIVED INHIBITOR (III) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRUZAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: CRUZIPAIN, CRUZAINE; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI; SOURCE 3 ORGANISM_TAXID: 5693; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: DH5ALPHA KEYWDS CYSTEINE PROTEASE, COVALENT INHIBITOR, VINYL SULFONE- KEYWDS 2 DERIVED, P1' POCKET, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.S.BRINEN,E.HANSELL,W.R.ROUSH,J.H.MCKERROW,R.J.FLETTERICK REVDAT 2 24-FEB-09 1F2B 1 VERSN REVDAT 1 26-JUL-00 1F2B 0 JRNL AUTH L.S.BRINEN,E.HANSELL,J.CHENG,W.R.ROUSH, JRNL AUTH 2 J.H.MCKERROW,R.J.FLETTERICK JRNL TITL A TARGET WITHIN THE TARGET: PROBING CRUZAIN'S P1' JRNL TITL 2 SITE TO DEFINE STRUCTURAL DETERMINANTS FOR THE JRNL TITL 3 CHAGAS' DISEASE PROTEASE. JRNL REF STRUCTURE FOLD.DES. V. 8 831 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10997902 JRNL DOI 10.1016/S0969-2126(00)00173-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.E.MCGRATH,A.E.EAKIN,J.C.ENGEL,J.H.MCKERROW, REMARK 1 AUTH 2 C.S.CRAIK,R.J.FLETTERICK REMARK 1 TITL THE CRYSTAL STRUCTURE OF CRUZAIN: A THERAPEUTIC REMARK 1 TITL 2 TARGET FOR CHAGAS' DISEASE REMARK 1 REF J.MOL.BIOL. V. 247 251 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1994.0137 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 79.9 REMARK 3 NUMBER OF REFLECTIONS : 19258 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1519 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1593 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.60 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.93 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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: NULL REMARK 4 REMARK 4 1F2B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-00. REMARK 100 THE RCSB ID CODE IS RCSB011157. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-98 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 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 : 15513 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE; MICRO SEEDING, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.68000 REMARK 290 SMTRY3 2 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 ALA A 89 33.09 -141.93 REMARK 500 ASP A 158 9.77 -150.86 REMARK 500 THR A 178 170.25 71.47 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 VS3 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F29 RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO VS1. REMARK 900 RELATED ID: 1F2A RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO VS2. REMARK 900 RELATED ID: 1F2C RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO VS4. REMARK 900 RELATED ID: 1AIM RELATED DB: PDB REMARK 900 CONTAINS SAME PROTEIN BOUND TO FMK INHIBITOR REMARK 900 RELATED ID: 2AIM RELATED DB: PDB REMARK 900 CONTAINS SAME PROTEIN BOUND TO FMK INHIBITOR REMARK 900 RELATED ID: 1EWL RELATED DB: PDB REMARK 900 SAME PROTEIN, WRR-99 INHIBITOR REMARK 900 RELATED ID: 1EWM RELATED DB: PDB REMARK 900 SAME PROTEIN, WRR-112 INHIBITOR REMARK 900 RELATED ID: 1EWO RELATED DB: PDB REMARK 900 SAME PROTEIN, WRR-204 INHIBITOR REMARK 900 RELATED ID: 1EWP RELATED DB: PDB REMARK 900 SAME PROTEIN, MOR-LEU-HPQ INHIBITOR DBREF 1F2B A 1 212 UNP P25779 CYSP_TRYCR 123 337 SEQRES 1 A 215 ALA PRO ALA ALA VAL ASP TRP ARG ALA ARG GLY ALA VAL SEQRES 2 A 215 THR ALA VAL LYS ASP GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 A 215 ALA PHE SER ALA ILE GLY ASN VAL GLU CYS GLN TRP PHE SEQRES 4 A 215 LEU ALA GLY HIS PRO LEU THR ASN LEU SER GLU GLN MET SEQRES 5 A 215 LEU VAL SER CYS ASP LYS THR ASP SER GLY CYS SER GLY SEQRES 6 A 215 GLY LEU MET ASN ASN ALA PHE GLU TRP ILE VAL GLN GLU SEQRES 7 A 215 ASN ASN GLY ALA VAL TYR THR GLU ASP SER TYR PRO TYR SEQRES 8 A 215 ALA SER GLY GLU GLY ILE SER PRO PRO CYS THR THR SER SEQRES 9 A 215 GLY HIS THR VAL GLY ALA THR ILE THR GLY HIS VAL GLU SEQRES 10 A 215 LEU PRO GLN ASP GLU ALA GLN ILE ALA ALA TRP LEU ALA SEQRES 11 A 215 VAL ASN GLY PRO VAL ALA VAL ALA VAL ASP ALA SER SER SEQRES 12 A 215 TRP MET THR TYR THR GLY GLY VAL MET THR SER CYS VAL SEQRES 13 A 215 SER GLU GLN LEU ASP HIS GLY VAL LEU LEU VAL GLY TYR SEQRES 14 A 215 ASN ASP SER ALA ALA VAL PRO TYR TRP ILE ILE LYS ASN SEQRES 15 A 215 SER TRP THR THR GLN TRP GLY GLU GLU GLY TYR ILE ARG SEQRES 16 A 215 ILE ALA LYS GLY SER ASN GLN CYS LEU VAL LYS GLU GLU SEQRES 17 A 215 ALA SER SER ALA VAL VAL GLY HET VS3 A 300 46 HETNAM VS3 3-[N-[BENZYLOXYCARBONYL]-PHENYLALANINYL-AMINO]-5- HETNAM 2 VS3 PHENYL-PENTANE-1-SULFONIC ACID 4-NITRO-PHENYL ESTER FORMUL 2 VS3 C34 H35 N3 O8 S FORMUL 3 HOH *66(H2 O) HELIX 1 1 ARG A 8 GLY A 11 5 4 HELIX 2 2 SER A 24 ALA A 41 1 18 HELIX 3 3 SER A 49 ASP A 57 1 9 HELIX 4 4 SER A 61 GLY A 65 5 5 HELIX 5 6 ASP A 116 GLY A 128 1 13 HELIX 6 7 ALA A 136 MET A 142 5 5 HELIX 7 8 ASN A 198 VAL A 202 5 5 SHEET 1 A 5 GLY A 109 GLU A 112 0 SHEET 2 A 5 ALA A 206 VAL A 210 -1 O SER A 208 N VAL A 111 SHEET 3 A 5 VAL A 130 VAL A 134 -1 O ALA A 131 N SER A 207 SHEET 4 A 5 HIS A 159 ASN A 167 -1 O HIS A 159 N VAL A 134 SHEET 5 A 5 ALA A 4 ASP A 6 -1 O VAL A 5 N TYR A 166 SHEET 1 B 7 GLY A 109 GLU A 112 0 SHEET 2 B 7 ALA A 206 VAL A 210 -1 O SER A 208 N VAL A 111 SHEET 3 B 7 VAL A 130 VAL A 134 -1 O ALA A 131 N SER A 207 SHEET 4 B 7 HIS A 159 ASN A 167 -1 O HIS A 159 N VAL A 134 SHEET 5 B 7 TYR A 170 LYS A 174 -1 O TYR A 170 N ASN A 167 SHEET 6 B 7 TYR A 186 ALA A 190 -1 O ILE A 187 N ILE A 173 SHEET 7 B 7 VAL A 148 MET A 149 1 O MET A 149 N ALA A 190 SHEET 1 C 2 ALA A 79 TYR A 81 0 SHEET 2 C 2 VAL A 102 THR A 106 -1 N GLY A 103 O VAL A 80 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.03 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.03 LINK C27 VS3 A 300 SG CYS A 25 1555 1555 1.83 SITE 1 AC1 17 GLN A 19 GLY A 23 CYS A 25 TRP A 26 SITE 2 AC1 17 SER A 61 CYS A 63 SER A 64 GLY A 65 SITE 3 AC1 17 GLY A 66 ALA A 133 ALA A 136 SER A 139 SITE 4 AC1 17 MET A 142 LEU A 157 ASP A 158 HIS A 159 SITE 5 AC1 17 TRP A 177 CRYST1 45.180 51.360 45.560 90.00 116.17 90.00 P 1 21 1 2 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 0.022134 0.000000 0.010877 0.00000 SCALE2 0.000000 0.019470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024456 0.00000