HEADER HYDROLASE 07-AUG-02 1ME4 TITLE HIGH RESOLUTION CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN NON-COVALENTLY TITLE 2 BOUND TO A HYDROXYMETHYL KETONE INHIBITOR (I) 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 4 11-OCT-17 1ME4 1 REMARK REVDAT 3 13-JUL-11 1ME4 1 VERSN REVDAT 2 24-FEB-09 1ME4 1 VERSN REVDAT 1 18-DEC-02 1ME4 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) : 0.096 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 52264 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.090 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.091 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.124 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1631 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 47929 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 : 34 REMARK 3 SOLVENT ATOMS : 484 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) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.077 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.083 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.068 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.083 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 1ME4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-02 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) : 0.980 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 : 51125 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.7000 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 (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.13000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.020 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 1F29 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.29 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 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 25.85600 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER 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 LEU A 163 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 GLU A 204 OE1 - CD - OE2 ANGL. DEV. = 8.1 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 THR A 178 164.87 80.68 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 T10 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 (II) REMARK 900 RELATED ID: 1F2A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO VINYL SSULFONE 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: 1F2B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN BOUND TO VINYL SULFONE REMARK 900 DERIVED INHIBITOR (III) DBREF 1ME4 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 T10 A 300 34 HETNAM T10 [1-(1-BENZYL-3-HYDROXY-2-OXO-PROPYLCARBAMOYL)-2-PHENYL- HETNAM 2 T10 ETHYL]-CARBAMIC ACID BENZYL ESTER FORMUL 2 T10 C27 H28 N2 O5 FORMUL 3 HOH *484(H2 O) HELIX 1 1 ARG A 8 ARG A 10 5 3 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 187 N ILE A 173 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 2.06 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.06 LINK SG CYS A 25 C6 T10 A 300 1555 1555 1.98 SITE 1 AC1 12 GLN A 19 GLY A 23 SER A 24 CYS A 25 SITE 2 AC1 12 TRP A 26 SER A 61 GLY A 65 GLY A 66 SITE 3 AC1 12 ALA A 133 ASP A 158 HIS A 159 HOH A1248 CRYST1 42.523 51.712 46.040 90.00 116.53 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 0.023517 0.000000 0.011740 0.00000 SCALE2 0.000000 0.019338 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024277 0.00000