PDB Short entry for 1IY7 HEADER HYDROLASE 24-JUL-02 1IY7 TITLE CRYSTAL STRUCTURE OF CPA AND SULFAMIDE-BASED INHIBITOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBOXYPEPTIDASE A; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.17.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-INHIBITOR COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.J.KIM,J.R.WOO,J.D.PARK,D.H.KIM,S.E.RYU REVDAT 3 27-DEC-23 1IY7 1 REMARK LINK REVDAT 2 24-FEB-09 1IY7 1 VERSN REVDAT 1 28-JAN-03 1IY7 0 JRNL AUTH J.D.PARK,D.H.KIM,S.J.KIM,J.R.WOO,S.E.RYU JRNL TITL SULFAMIDE-BASED INHIBITORS FOR CARBOXYPEPTIDASE A. NOVEL JRNL TITL 2 TYPE TRANSITION STATE ANALOGUE INHIBITORS FOR ZINC PROTEASES JRNL REF J.MED.CHEM. V. 45 5295 2002 JRNL REFN ISSN 0022-2623 JRNL PMID 12431056 JRNL DOI 10.1021/JM020258V REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 19491 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 SET) : 0.175 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 945 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2280 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE : 0.2130 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 117 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2436 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -1.20000 REMARK 3 B33 (A**2) : 1.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.86000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 44.72 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IY7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000005397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL 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 : CONFOCAL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 26.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 30.23350 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 GLU A 122 -39.95 -133.16 REMARK 500 SER A 135 59.79 -99.10 REMARK 500 SER A 136 149.47 -171.57 REMARK 500 SER A 199 -0.83 120.15 REMARK 500 GLN A 200 75.25 53.05 REMARK 500 ILE A 247 -59.89 -126.98 REMARK 500 TYR A 248 166.30 177.29 REMARK 500 ASP A 273 -142.47 -111.43 REMARK 500 LEU A 280 46.76 -97.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 308 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 69 ND1 REMARK 620 2 GLU A 72 OE2 122.2 REMARK 620 3 GLU A 72 OE1 95.9 55.0 REMARK 620 4 HIS A 196 ND1 98.9 92.7 147.4 REMARK 620 5 CXA A 500 N19 120.4 105.2 82.7 113.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CXA A 500 DBREF 1IY7 A 1 307 UNP P00730 CBPA1_BOVIN 111 417 SEQRES 1 A 307 ALA ARG SER THR ASN THR PHE ASN TYR ALA THR TYR HIS SEQRES 2 A 307 THR LEU ASP GLU ILE TYR ASP PHE MET ASP LEU LEU VAL SEQRES 3 A 307 ALA GLN HIS PRO GLU LEU VAL SER LYS LEU GLN ILE GLY SEQRES 4 A 307 ARG SER TYR GLU GLY ARG PRO ILE TYR VAL LEU LYS PHE SEQRES 5 A 307 SER THR GLY GLY SER ASN ARG PRO ALA ILE TRP ILE ASP SEQRES 6 A 307 LEU GLY ILE HIS SER ARG GLU TRP ILE THR GLN ALA THR SEQRES 7 A 307 GLY VAL TRP PHE ALA LYS LYS PHE THR GLU ASN TYR GLY SEQRES 8 A 307 GLN ASN PRO SER PHE THR ALA ILE LEU ASP SER MET ASP SEQRES 9 A 307 ILE PHE LEU GLU ILE VAL THR ASN PRO ASN GLY PHE ALA SEQRES 10 A 307 PHE THR HIS SER GLU ASN ARG LEU TRP ARG LYS THR ARG SEQRES 11 A 307 SER VAL THR SER SER SER LEU CYS VAL GLY VAL ASP ALA SEQRES 12 A 307 ASN ARG ASN TRP ASP ALA GLY PHE GLY LYS ALA GLY ALA SEQRES 13 A 307 SER SER SER PRO CYS SER GLU THR TYR HIS GLY LYS TYR SEQRES 14 A 307 ALA ASN SER GLU VAL GLU VAL LYS SER ILE VAL ASP PHE SEQRES 15 A 307 VAL LYS ASN HIS GLY ASN PHE LYS ALA PHE LEU SER ILE SEQRES 16 A 307 HIS SER TYR SER GLN LEU LEU LEU TYR PRO TYR GLY TYR SEQRES 17 A 307 THR THR GLN SER ILE PRO ASP LYS THR GLU LEU ASN GLN SEQRES 18 A 307 VAL ALA LYS SER ALA VAL ALA ALA LEU LYS SER LEU TYR SEQRES 19 A 307 GLY THR SER TYR LYS TYR GLY SER ILE ILE THR THR ILE SEQRES 20 A 307 TYR GLN ALA SER GLY GLY SER ILE ASP TRP SER TYR ASN SEQRES 21 A 307 GLN GLY ILE LYS TYR SER PHE THR PHE GLU LEU ARG ASP SEQRES 22 A 307 THR GLY ARG TYR GLY PHE LEU LEU PRO ALA SER GLN ILE SEQRES 23 A 307 ILE PRO THR ALA GLN GLU THR TRP LEU GLY VAL LEU THR SEQRES 24 A 307 ILE MET GLU HIS THR VAL ASN ASN HET ZN A 308 1 HET CXA A 500 16 HETNAM ZN ZINC ION HETNAM CXA PHENYLALANINE-N-SULFONAMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 CXA C9 H12 N2 O4 S FORMUL 4 HOH *148(H2 O) HELIX 1 1 THR A 14 HIS A 29 1 16 HELIX 2 2 GLU A 72 TYR A 90 1 19 HELIX 3 3 ASN A 93 MET A 103 1 11 HELIX 4 4 ASN A 112 GLU A 122 1 11 HELIX 5 5 GLU A 173 GLY A 187 1 15 HELIX 6 6 ASP A 215 SER A 232 1 18 HELIX 7 7 ILE A 243 ILE A 247 1 5 HELIX 8 8 GLY A 253 GLN A 261 1 9 HELIX 9 9 TYR A 277 LEU A 281 5 5 HELIX 10 10 PRO A 282 SER A 284 5 3 HELIX 11 11 GLN A 285 ASN A 306 1 22 SHEET 1 A 8 VAL A 33 ARG A 40 0 SHEET 2 A 8 PRO A 46 PHE A 52 -1 O VAL A 49 N LEU A 36 SHEET 3 A 8 ASP A 104 GLU A 108 -1 O ILE A 105 N PHE A 52 SHEET 4 A 8 ALA A 61 LEU A 66 1 N ILE A 62 O PHE A 106 SHEET 5 A 8 PHE A 189 HIS A 196 1 O ILE A 195 N ASP A 65 SHEET 6 A 8 TYR A 265 GLU A 270 1 O PHE A 269 N HIS A 196 SHEET 7 A 8 LEU A 201 TYR A 204 -1 N LEU A 203 O THR A 268 SHEET 8 A 8 LYS A 239 SER A 242 1 O LYS A 239 N LEU A 202 SSBOND 1 CYS A 138 CYS A 161 1555 1555 2.02 LINK ND1 HIS A 69 ZN ZN A 308 1555 1555 2.02 LINK OE2 GLU A 72 ZN ZN A 308 1555 1555 2.46 LINK OE1 GLU A 72 ZN ZN A 308 1555 1555 2.26 LINK ND1 HIS A 196 ZN ZN A 308 1555 1555 2.15 LINK ZN ZN A 308 N19 CXA A 500 1555 1555 1.92 CISPEP 1 SER A 197 TYR A 198 0 -0.39 CISPEP 2 PRO A 205 TYR A 206 0 0.25 CISPEP 3 ARG A 272 ASP A 273 0 -0.70 SITE 1 AC1 4 HIS A 69 GLU A 72 HIS A 196 CXA A 500 SITE 1 AC2 12 HIS A 69 GLU A 72 ARG A 127 ASN A 144 SITE 2 AC2 12 ARG A 145 HIS A 196 SER A 197 ILE A 243 SITE 3 AC2 12 TYR A 248 THR A 268 GLU A 270 ZN A 308 CRYST1 51.688 60.467 47.256 90.00 82.55 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 0.019347 0.000000 -0.002530 0.00000 SCALE2 0.000000 0.016538 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021341 0.00000