HEADER HYDROLASE 04-OCT-00 1FZZ TITLE THE CRYSTAL STRUCTURE OF THE COMPLEX OF NON-PEPTIDIC INHIBITOR ONO- TITLE 2 6818 AND PORCINE PANCREATIC ELASTASE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELASTASE 1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.36 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 ORGAN: PANCREAS KEYWDS ENZYME-INHIBITOR COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ODAGAKI,K.OHMOTO,S.MATSUOKA,N.HAMANAKA,H.NAKAI,M.TODA,Y.KATSUYA REVDAT 3 04-OCT-17 1FZZ 1 REMARK REVDAT 2 24-FEB-09 1FZZ 1 VERSN REVDAT 1 04-OCT-01 1FZZ 0 JRNL AUTH Y.ODAGAKI,K.OHMOTO,S.MATSUOKA,N.HAMANAKA,H.NAKAI,M.TODA, JRNL AUTH 2 Y.KATSUYA JRNL TITL THE CRYSTAL STRUCTURE OF THE COMPLEX OF NON-PEPTIDIC JRNL TITL 2 INHIBITOR OF HUMAN NEUTROPHIL ELASTASE ONO-6818 AND PORCINE JRNL TITL 3 PANCREATIC ELASTASE. JRNL REF BIOORG.MED.CHEM. V. 9 647 2001 JRNL REFN ISSN 0968-0896 JRNL PMID 11310599 JRNL DOI 10.1016/S0968-0896(00)00277-7 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 19409 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) : 0.198 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1724 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 : 1822 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.330 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 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 1FZZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.0 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 RU200 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 : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19409 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.380 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 1.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.41 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 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 (%): 43.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM SULFATE, SODIUM ACETATE, PH REMARK 280 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 25.51900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.82150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.82150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.51900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.25000 REMARK 290 SMTRY3 4 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 HIS A 71 -53.49 -128.47 REMARK 500 THR A 79 -4.09 -140.48 REMARK 500 THR A 96 136.39 -36.79 REMARK 500 ASP A 97 -10.02 63.18 REMARK 500 TYR A 171 -111.52 -108.13 REMARK 500 SER A 189 176.40 178.46 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 681 A 395 DBREF 1FZZ A 16 245 UNP P00772 ELA1_PIG 27 266 SEQRES 1 A 240 VAL VAL GLY GLY THR GLU ALA GLN ARG ASN SER TRP PRO SEQRES 2 A 240 SER GLN ILE SER LEU GLN TYR ARG SER GLY SER SER TRP SEQRES 3 A 240 ALA HIS THR CYS GLY GLY THR LEU ILE ARG GLN ASN TRP SEQRES 4 A 240 VAL MET THR ALA ALA HIS CYS VAL ASP ARG GLU LEU THR SEQRES 5 A 240 PHE ARG VAL VAL VAL GLY GLU HIS ASN LEU ASN GLN ASN SEQRES 6 A 240 ASP GLY THR GLU GLN TYR VAL GLY VAL GLN LYS ILE VAL SEQRES 7 A 240 VAL HIS PRO TYR TRP ASN THR ASP ASP VAL ALA ALA GLY SEQRES 8 A 240 TYR ASP ILE ALA LEU LEU ARG LEU ALA GLN SER VAL THR SEQRES 9 A 240 LEU ASN SER TYR VAL GLN LEU GLY VAL LEU PRO ARG ALA SEQRES 10 A 240 GLY THR ILE LEU ALA ASN ASN SER PRO CYS TYR ILE THR SEQRES 11 A 240 GLY TRP GLY LEU THR ARG THR ASN GLY GLN LEU ALA GLN SEQRES 12 A 240 THR LEU GLN GLN ALA TYR LEU PRO THR VAL ASP TYR ALA SEQRES 13 A 240 ILE CYS SER SER SER SER TYR TRP GLY SER THR VAL LYS SEQRES 14 A 240 ASN SER MET VAL CYS ALA GLY GLY ASP GLY VAL ARG SER SEQRES 15 A 240 GLY CYS GLN GLY ASP SER GLY GLY PRO LEU HIS CYS LEU SEQRES 16 A 240 VAL ASN GLY GLN TYR ALA VAL HIS GLY VAL THR SER PHE SEQRES 17 A 240 VAL SER ARG LEU GLY CYS ASN VAL THR ARG LYS PRO THR SEQRES 18 A 240 VAL PHE THR ARG VAL SER ALA TYR ILE SER TRP ILE ASN SEQRES 19 A 240 ASN VAL ILE ALA SER ASN HET 681 A 395 33 HETNAM 681 2-(5-AMINO-6-OXO-2-PHENYL-6H-PYRIMIDIN-1-YL)-N-[2-(5- HETNAM 2 681 TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)-1-(METHYLETHYL)-2- HETNAM 3 681 HYDROXYETHYL]ACETAMIDE HETSYN 681 ONO-6818 FORMUL 2 681 C23 H30 N6 O4 FORMUL 3 HOH *64(H2 O) HELIX 1 1 ALA A 55 VAL A 59 5 5 HELIX 2 2 ASP A 98 GLY A 100 5 5 HELIX 3 3 ASP A 164 SER A 169 1 6 HELIX 4 4 TRP A 172 VAL A 176 5 5 HELIX 5 5 TYR A 234 SER A 244 1 11 SHEET 1 A 8 THR A 20 GLU A 21 0 SHEET 2 A 8 GLN A 156 TYR A 159 -1 O GLN A 157 N THR A 20 SHEET 3 A 8 CYS A 136 GLY A 140 -1 N ILE A 138 O ALA A 158 SHEET 4 A 8 PRO A 198 VAL A 203 -1 O PRO A 198 N THR A 139 SHEET 5 A 8 GLN A 206 PHE A 215 -1 O GLN A 206 N VAL A 203 SHEET 6 A 8 THR A 226 ARG A 230 -1 N VAL A 227 O PHE A 215 SHEET 7 A 8 MET A 180 ALA A 183 -1 O VAL A 181 N PHE A 228 SHEET 8 A 8 THR A 162 VAL A 163 -1 N VAL A 163 O CYS A 182 SHEET 1 B 7 SER A 37 ARG A 48 0 SHEET 2 B 7 TRP A 51 THR A 54 -1 O TRP A 51 N ILE A 47 SHEET 3 B 7 ALA A 104 LEU A 108 -1 O ALA A 104 N THR A 54 SHEET 4 B 7 GLN A 81 VAL A 90 -1 N GLN A 86 O ARG A 107 SHEET 5 B 7 PHE A 65 VAL A 68 -1 O PHE A 65 N VAL A 85 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 2 CYS A 136 CYS A 201 1555 1555 2.03 SSBOND 3 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 4 CYS A 191 CYS A 220 1555 1555 2.04 LINK OG SER A 195 C1 681 A 395 1555 1555 1.44 LINK OG SER A 195 O1 681 A 395 1555 1555 2.03 SITE 1 AC1 11 HIS A 57 CYS A 191 GLN A 192 GLY A 193 SITE 2 AC1 11 ASP A 194 SER A 195 THR A 213 SER A 214 SITE 3 AC1 11 PHE A 215 VAL A 216 HOH A 281 CRYST1 51.038 58.500 75.643 90.00 90.00 90.00 P 21 21 21 4 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 0.019593 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013220 0.00000