HEADER HYDROLASE 07-AUG-02 1ME3 TITLE HIGH RESOLUTION CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN NON-COVALENTLY TITLE 2 BOUND TO A HYDROXYMETHYL KETONE INHIBITOR (II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRUZIPAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: MAJOR CYSTEINE PROTEINASE, CRUZAINE, CRUZAIN; 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_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: DH5ALPHA KEYWDS CYSTEINE PROTEASE, NON-COVALENT INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.S.BRINEN,L.HUANG,J.A.ELLMAN REVDAT 3 11-OCT-17 1ME3 1 REMARK REVDAT 2 24-FEB-09 1ME3 1 VERSN REVDAT 1 18-DEC-02 1ME3 0 JRNL AUTH L.HUANG,L.S.BRINEN,J.A.ELLMAN JRNL TITL CRYSTAL STRUCTURES OF REVERSIBLE KETONE-BASED INHIBITORS OF JRNL TITL 2 THE CYSTEINE PROTEASE CRUZAIN JRNL REF BIOORG.MED.CHEM. V. 11 21 2003 JRNL REFN ISSN 0968-0896 JRNL PMID 12467703 JRNL DOI 10.1016/S0968-0896(02)00427-3 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.S.BRINEN,E.HANSELL,J.CHENG,W.R.ROUSH,J.H.MCKERROW, REMARK 1 AUTH 2 R.J.FLETTERICK REMARK 1 TITL A TARGET WITHIN THE TARGET: PROBING CRUZAIN'S P1' SITE TO REMARK 1 TITL 2 DEFINE STRUCTURAL DETERMINANTS FOR THE CHAGAS' DISEASE REMARK 1 TITL 3 PROTEASE REMARK 1 REF STRUCTURE V. 8 831 2000 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(00)00173-8 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.E.MCGRATH,A.E.EAKIN,J.C.ENGEL,J.H.MCKERROW,C.S.CRAIK, REMARK 1 AUTH 2 R.J.FLETTERICK REMARK 1 TITL THE CRYSTAL STRUCTURE OF CRUZAIN: A THERAPEUTIC TARGET FOR REMARK 1 TITL 2 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.105 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.103 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.135 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4792 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 42575 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)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 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 : 35 REMARK 3 SOLVENT ATOMS : 548 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.034 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.076 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.078 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.017 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.079 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 1ME3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.06500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.80 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: PDB ENTRY 1F2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6 - 1.0 M SODIUM CITRATE, PH 6.8, REMARK 280 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 25.79500 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: 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 84 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 VAL A 102 CA - CB - CG1 ANGL. DEV. = 9.1 DEGREES REMARK 500 GLU A 204 OE1 - CD - OE2 ANGL. DEV. = 11.1 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 TYR A 86 69.64 -150.72 REMARK 500 SER A 152 40.16 71.17 REMARK 500 THR A 178 167.12 77.51 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 P10 A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F29 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO A VINYL SULFONE REMARK 900 DERIVED INHIBITOR (I) REMARK 900 RELATED ID: 1F2A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO A VINYL SULFONE REMARK 900 DERIVED INHIBITOR (II) REMARK 900 RELATED ID: 1F2B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO VINYL SULFONE REMARK 900 DERIVED INHIBITOR (III) REMARK 900 RELATED ID: 1F2C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO VINYL SULFONE REMARK 900 DERIVED INHIBITOR (IV) REMARK 900 RELATED ID: 1ME4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO A HYDROXYMETHYL REMARK 900 KETONE INHIBITOR (I) DBREF 1ME3 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 P10 A 300 35 HETNAM P10 [1-(3-HYDROXY-2-OXO-1-PHENETHYL-PROPYLCARBAMOYL)2- HETNAM 2 P10 PHENYL-ETHYL]-CARBAMIC ACID PYRIDIN-4-YLMETHYL ESTER FORMUL 2 P10 C27 H29 N3 O5 FORMUL 3 HOH *548(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 5 LEU A 67 ASN A 78A 1 13 HELIX 6 6 ASP A 116 GLY A 128 1 13 HELIX 7 7 SER A 140 TYR A 144 5 5 HELIX 8 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 N ALA A 131 O SER A 207 SHEET 4 A 5 HIS A 159 ASN A 167 -1 O LEU A 163 N VAL A 130 SHEET 5 A 5 ALA A 4 ASP A 6 -1 N VAL A 5 O 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 N ALA A 131 O SER A 207 SHEET 4 B 7 HIS A 159 ASN A 167 -1 O LEU A 163 N VAL A 130 SHEET 5 B 7 TYR A 170 LYS A 174 -1 O LYS A 174 N LEU A 162 SHEET 6 B 7 TYR A 186 ALA A 190 -1 O ILE A 189 N TRP A 171 SHEET 7 B 7 VAL A 148 MET A 149 1 N MET A 149 O ARG A 188 SHEET 1 C 2 ALA A 79 TYR A 81 0 SHEET 2 C 2 VAL A 102 THR A 106 -1 O GLY A 103 N VAL A 80 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.06 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.07 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.05 LINK SG CYS A 25 C2 P10 A 300 1555 1555 2.00 SITE 1 AC1 15 GLN A 19 GLY A 23 SER A 24 CYS A 25 SITE 2 AC1 15 TRP A 26 SER A 61 GLY A 65 GLY A 66 SITE 3 AC1 15 LEU A 67 ALA A 133 ASP A 158 HIS A 159 SITE 4 AC1 15 HOH A1067 HOH A1202 HOH A1311 CRYST1 42.570 51.590 45.950 90.00 116.62 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 0.023491 0.000000 0.011773 0.00000 SCALE2 0.000000 0.019384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024343 0.00000