HEADER SERINE PROTEASE 24-AUG-98 1BRU TITLE STRUCTURE OF PORCINE PANCREATIC ELASTASE COMPLEXED WITH THE ELASTASE TITLE 2 INHIBITOR GR143783 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELASTASE; COMPND 3 CHAIN: P; COMPND 4 SYNONYM: PPE; COMPND 5 EC: 3.4.21.71; COMPND 6 OTHER_DETAILS: INHIBITOR GR143783 COVALENTLY ATTACHED TO PPE, BOND COMPND 7 BETWEEN C 30 (INHIBITOR) AND OG SER 195 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 SERINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.JHOTI,O.M.P.SINGH,A.WONACOTT REVDAT 3 18-APR-18 1BRU 1 REMARK REVDAT 2 24-FEB-09 1BRU 1 VERSN REVDAT 1 25-AUG-99 1BRU 0 JRNL AUTH H.JHOTI,O.M.P.SINGH,A.WONACOTT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 5000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1817 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 194 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.700 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 1BRU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-92 REMARK 200 TEMPERATURE (KELVIN) : 287 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 : ELLIOTT GX-21 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 : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNESS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8677 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.0 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 20.79500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.11500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.22500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.11500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.79500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.22500 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: P 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER P 195 O5 1NB P 1 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP P 51 CE2 TRP P 51 CD2 0.077 REMARK 500 SER P 195 CB SER P 195 OG -0.201 REMARK 500 REMARK 500 REMARK: NULL 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 VAL P 31 CA - CB - CG1 ANGL. DEV. = 9.5 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 TRP P 27 75.04 -119.06 REMARK 500 HIS P 71 -60.90 -123.28 REMARK 500 ASN P 147 7.50 56.19 REMARK 500 TRP P 171 -111.53 -95.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CATALYTIC TRIAD REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1NB P 1 DBREF 1BRU P 16 245 UNP P08419 ELA2_PIG 29 269 SEQRES 1 P 241 VAL VAL GLY GLY GLU ASP ALA ARG PRO ASN SER TRP PRO SEQRES 2 P 241 TRP GLN VAL SER LEU GLN TYR ASP SER SER GLY GLN TRP SEQRES 3 P 241 ARG HIS THR CYS GLY GLY THR LEU VAL ASP GLN SER TRP SEQRES 4 P 241 VAL LEU THR ALA ALA HIS CYS ILE SER SER SER ARG THR SEQRES 5 P 241 TYR ARG VAL VAL LEU GLY ARG HIS SER LEU SER THR ASN SEQRES 6 P 241 GLU PRO GLY SER LEU ALA VAL LYS VAL SER LYS LEU VAL SEQRES 7 P 241 VAL HIS GLN ASP TRP ASN SER ASN GLN LEU SER ASN GLY SEQRES 8 P 241 ASN ASP ILE ALA LEU LEU LYS LEU ALA SER PRO VAL SER SEQRES 9 P 241 LEU THR ASP LYS ILE GLN LEU GLY CYS LEU PRO ALA ALA SEQRES 10 P 241 GLY THR ILE LEU PRO ASN ASN TYR VAL CYS TYR VAL THR SEQRES 11 P 241 GLY TRP GLY ARG LEU GLN THR ASN GLY ALA SER PRO ASP SEQRES 12 P 241 ILE LEU GLN GLN GLY GLN LEU LEU VAL VAL ASP TYR ALA SEQRES 13 P 241 THR CYS SER LYS PRO GLY TRP TRP GLY SER THR VAL LYS SEQRES 14 P 241 THR ASN MET ILE CYS ALA GLY GLY ASP GLY ILE ILE SER SEQRES 15 P 241 SER CYS ASN GLY ASP SER GLY GLY PRO LEU ASN CYS GLN SEQRES 16 P 241 GLY ALA ASN GLY GLN TRP GLN VAL HIS GLY ILE VAL SER SEQRES 17 P 241 PHE GLY SER SER LEU GLY CYS ASN TYR TYR HIS LYS PRO SEQRES 18 P 241 SER VAL PHE THR ARG VAL SER ASN TYR ILE ASP TRP ILE SEQRES 19 P 241 ASN SER VAL ILE ALA ASN ASN HET 1NB P 1 12 HETNAM 1NB 2-(2-HYDROXY-CYCLOPENTYL)-PENT-4-ENAL HETSYN 1NB GR143783 FORMUL 2 1NB C10 H16 O2 FORMUL 3 HOH *194(H2 O) HELIX 1 1 ALA P 56 CYS P 58 5 3 HELIX 2 2 LEU P 99 ASN P 99B 5 3 HELIX 3 3 TYR P 165 CYS P 168 1 4 HELIX 4 4 GLY P 173 THR P 175 5 3 HELIX 5 5 VAL P 231 ASN P 233 5 3 HELIX 6 6 ILE P 235 ALA P 243 1 9 SHEET 1 A 7 LEU P 81 LYS P 84 0 SHEET 2 A 7 TYR P 65 LEU P 68 -1 N LEU P 68 O LEU P 81 SHEET 3 A 7 GLN P 30 SER P 36A-1 N GLN P 34 O ARG P 65A SHEET 4 A 7 GLN P 37 ASP P 48 -1 N GLY P 44 O VAL P 31 SHEET 5 A 7 TRP P 51 THR P 54 -1 N LEU P 53 O THR P 45 SHEET 6 A 7 ALA P 104 LEU P 108 -1 N LEU P 106 O VAL P 52 SHEET 7 A 7 VAL P 85 VAL P 90 -1 N VAL P 89 O LEU P 105 SHEET 1 B 6 GLN P 156 LEU P 161 0 SHEET 2 B 6 VAL P 135 GLY P 140 -1 N GLY P 140 O GLN P 156 SHEET 3 B 6 PRO P 198 GLN P 202 -1 N ASN P 200 O TYR P 137 SHEET 4 B 6 TRP P 207 PHE P 215 -1 N GLY P 211 O LEU P 199 SHEET 5 B 6 SER P 226 ARG P 230 -1 N THR P 229 O ILE P 212 SHEET 6 B 6 MET P 180 ALA P 183 -1 N ALA P 183 O SER P 226 SSBOND 1 CYS P 42 CYS P 58 1555 1555 1.96 SSBOND 2 CYS P 136 CYS P 201 1555 1555 2.02 SSBOND 3 CYS P 168 CYS P 182 1555 1555 2.03 SSBOND 4 CYS P 191 CYS P 220 1555 1555 2.06 LINK C30 1NB P 1 OG SER P 195 1555 1555 1.24 SITE 1 CAT 1 SER P 195 SITE 1 AC1 9 HIS P 57 SER P 190 CYS P 191 ASN P 192 SITE 2 AC1 9 GLY P 193 ASP P 194 SER P 195 SER P 214 SITE 3 AC1 9 HOH P 367 CRYST1 41.590 46.450 128.230 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 0.024044 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007798 0.00000