HEADER BLOOD CLOTTING,HYDROLASE/INHIBITOR 09-SEP-03 1O5G TITLE DISSECTING AND DESIGNING INHIBITOR SELECTIVITY DETERMINANTS AT THE S1 TITLE 2 SITE USING AN ARTIFICIAL ALA190 PROTEASE (ALA190 UPA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: LIGHT CHAIN, RESIDUES 328-363; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTHROMBIN; COMPND 9 CHAIN: H; COMPND 10 FRAGMENT: HEAVY CHAIN, RESIDUES 364-620; COMPND 11 SYNONYM: COAGULATION FACTOR II; COMPND 12 EC: 3.4.21.5; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HIRUDIN IIIB'; COMPND 15 CHAIN: I; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 12 ORGANISM_TAXID: 6421 KEYWDS ALA190 UPA, S1 SITE, SELECTIVITY, CONSERVED WATER DISPLACEMENT KEYWDS 2 HYDROGEN BOND DEFICIT, TRYPSIN, THROMBIN, HEPSIN, FACTOR VIIA, BLOOD KEYWDS 3 CLOTTING, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, BLOOD KEYWDS 4 CLOTTING,HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.A.KATZ,C.LUONG,J.D.HO,J.R.SOMOZA,E.GJERSTAD,J.TANG,S.R.WILLIAMS, AUTHOR 2 E.VERNER,R.L.MACKMAN,W.B.YOUNG,P.A.SPRENGELER,H.CHAN,K.MORTARA, AUTHOR 3 J.W.JANC,M.E.MCGRATH REVDAT 4 13-JUL-11 1O5G 1 VERSN REVDAT 3 24-FEB-09 1O5G 1 VERSN REVDAT 2 10-MAY-05 1O5G 1 JRNL REVDAT 1 21-SEP-04 1O5G 0 JRNL AUTH B.A.KATZ,C.LUONG,J.D.HO,J.R.SOMOZA,E.GJERSTAD,J.TANG, JRNL AUTH 2 S.R.WILLIAMS,E.VERNER,R.L.MACKMAN,W.B.YOUNG,P.A.SPRENGELER, JRNL AUTH 3 H.CHAN,K.MORTARA,J.W.JANC,M.E.MCGRATH JRNL TITL DISSECTING AND DESIGNING INHIBITOR SELECTIVITY DETERMINANTS JRNL TITL 2 AT THE S1 SITE USING AN ARTIFICIAL ALA190 PROTEASE (ALA190 JRNL TITL 3 UPA). JRNL REF J.MOL.BIOL. V. 344 527 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15522303 JRNL DOI 10.1016/J.JMB.2004.09.032 REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.100 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 74.3 REMARK 3 NUMBER OF REFLECTIONS : 26771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2688 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 : 2392 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 118 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 3.60 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: REMARK 3 ASP_H21, MET_H84, HIS_H119, VAL_H157 WERE SIMULTANEOUSLY REFINED IN REMARK 3 TWO CONFORMATIONS. REMARK 3 REMARK 3 RESIDUES AFTER ILE_L16K (LIGHT CHAIN) HAVE WEAK OR NO DENSITY, AND REMARK 3 ARE REMARK 3 NOT INCLUDED IN THE MODEL. REMARK 3 REMARK 3 DENSITY IS ABSENT FOR THE LAST TWO RESIDUES OF THE HEAVY CHAIN, REMARK 3 WHICH REMARK 3 ARE NOT INCLUDED IN THE MODEL. REMARK 3 REMARK 3 NO DENSITY WAS OBSERVED FOR THR147, TRP148, THR149, ALA149A, REMARK 3 ASN149B, VAL149C, REMARK 3 GLY149D, AND LYS149E IN THE AUTOLYSIS LOOP, AND THESE RESIDUES ARE REMARK 3 NOT REMARK 3 INCLUDED IN THE MODEL. REMARK 3 REMARK 3 IN THE NON-ACTIVE SITE PEPTIDE INHIBITOR (ACETYLHIRUDIN) REMARK 3 THE TYROSINE HYDROXYL IS SULFONATED. REMARK 3 REMARK 3 HOH477, OGSER195 AND O6' AND N3 OF THE INHIBITOR MAKE A 3-CENTERED REMARK 3 SHORT REMARK 3 HYDROGEN BOND ARRAY. REMARK 3 REMARK 3 DISORDERED WATERS INCLUDE: REMARK 3 HOH_395 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF. REMARK 3 REMARK 3 AHOH_393 IS CLOSE TO BHOH_393. REMARK 3 AHOH_394 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF. REMARK 3 BHOH_395 IS CLOSE TO A SYMMETRY RELATED EQUIVALENT OF ITSELF. REMARK 3 HOH_393, HOH_394, AND HOH_395 FORM A CLUSTER OF DENSITY REMARK 3 DENSITY FOR THESE "WATERS" IS GREATER THAN FOR REAL WATERS, REMARK 3 SO OCCUPANCIES WERE REFINED. REMARK 3 REMARK 3 AHOH_674 IS CLOSE TO BHOH_674. REMARK 4 REMARK 4 1O5G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-03. REMARK 100 THE RCSB ID CODE IS RCSB001826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 285 REMARK 200 PH : 7.50 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 RUH3R 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 : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35940 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 27.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: QUANTA REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-PROPANOL, PEG 4000, PH 6.5, VAPOR REMARK 280 DIFFUSION AT 298 K, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.67000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.02000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.67000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.02000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH H 394 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 396 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 395 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 REMARK 465 TRP H 147A REMARK 465 THR H 147B REMARK 465 ALA H 147C REMARK 465 ASN H 147D REMARK 465 VAL H 147E REMARK 465 GLY H 147F REMARK 465 LYS H 147G REMARK 465 GLY H 246 REMARK 465 GLU H 247 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 HG SER H 195 HN3 CR9 H 393 1.07 REMARK 500 OG SER H 195 H2 HOH H 445 1.20 REMARK 500 HG SER H 195 O6' CR9 H 393 1.20 REMARK 500 OG SER H 195 HN3 CR9 H 393 1.38 REMARK 500 O6' CR9 H 393 H1 HOH H 445 1.45 REMARK 500 HG SER H 195 H1 HOH H 445 1.46 REMARK 500 HG SER H 195 H2 HOH H 445 1.47 REMARK 500 OG1 THR H 74 H2 HOH H 451 1.52 REMARK 500 O LYS H 110 H1 HOH H 481 1.53 REMARK 500 O ALA H 113 H2 HOH H 473 1.57 REMARK 500 F2 CR9 H 393 H1 HOH H 475 1.57 REMARK 500 OH TYR H 225 H2 HOH H 491 1.57 REMARK 500 O VAL H 163 H1 HOH H 413 1.58 REMARK 500 OG SER H 195 O HOH H 445 2.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HE ARG H 77A H1 HOH H 430 2555 1.50 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 HIS H 91 NE2 HIS H 91 CD2 -0.086 REMARK 500 HIS H 230 NE2 HIS H 230 CD2 -0.067 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 GLY L 1F N - CA - C ANGL. DEV. = -22.3 DEGREES REMARK 500 ARG L 4 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG H 35 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG H 97 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 CYS H 122 CA - CB - SG ANGL. DEV. = 8.2 DEGREES REMARK 500 TYR H 134 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG H 173 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 CYS H 182 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG H 187 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 PHE H 199 N - CA - C ANGL. DEV. = -19.1 DEGREES REMARK 500 ARG H 206 NE - CZ - NH2 ANGL. DEV. = -4.2 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 SER L 1E -65.44 -124.76 REMARK 500 GLU L 1C 30.24 -72.01 REMARK 500 ALA L 1B -44.91 67.86 REMARK 500 PHE L 7 -88.95 -126.24 REMARK 500 TYR H 60A 78.12 -152.21 REMARK 500 ASN H 60G 82.89 -161.30 REMARK 500 HIS H 71 -55.46 -131.25 REMARK 500 ASN H 78 -4.54 71.20 REMARK 500 ASP H 186A 52.19 -95.57 REMARK 500 SER H 195 140.60 -39.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG L 14D 0.10 SIDE CHAIN REMARK 500 ARG H 35 0.08 SIDE CHAIN REMARK 500 ARG H 50 0.10 SIDE CHAIN REMARK 500 ARG H 67 0.19 SIDE CHAIN REMARK 500 ARG H 75 0.15 SIDE CHAIN REMARK 500 ARG H 93 0.26 SIDE CHAIN REMARK 500 ARG H 126 0.23 SIDE CHAIN REMARK 500 ARG H 173 0.21 SIDE CHAIN REMARK 500 ARG H 187 0.19 SIDE CHAIN REMARK 500 ARG H 221A 0.11 SIDE CHAIN REMARK 500 ARG H 233 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H 488 DISTANCE = 5.26 ANGSTROMS 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 CA H 392 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE H 204A O REMARK 620 2 HOH H 477 O 81.3 REMARK 620 3 HOH H 484 O 81.2 96.7 REMARK 620 4 HOH H 424 O 172.1 104.2 92.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 391 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 96.9 REMARK 620 3 HOH H 433 O 89.8 82.9 REMARK 620 4 HOH H 431 O 89.8 166.7 108.7 REMARK 620 5 HOH H 411 O 161.3 69.0 100.1 101.8 REMARK 620 6 HOH H 414 O 88.3 90.4 172.7 78.3 79.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CR9 H 393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN IIIB' REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C5N RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT INHIBITOR DBREF 1O5G L 1H 17 UNP P00734 THRB_HUMAN 328 363 DBREF 1O5G H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1O5G I 55 65 UNP P28511 ITHK_HIRME 55 65 SEQADV 1O5G TYS I 63 UNP P28511 TYR 63 MODIFIED RESIDUE SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 I 11 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 1O5G TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 24 HET NA H 391 1 HET CA H 392 1 HET CR9 H 393 51 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETNAM CR9 2-{5-[AMINO(IMINIO)METHYL]-6-FLUORO-1H-BENZIMIDAZOL-2- HETNAM 2 CR9 YL}-6-[(2-METHYLCYCLOHEXYL)OXY]BENZENOLATE HETSYN CR9 CRA_11092 FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA NA 1+ FORMUL 5 CA CA 2+ FORMUL 6 CR9 C21 H23 F N4 O2 FORMUL 7 HOH *118(H2 O) HELIX 1 1 PHE L 7 SER L 11 5 5 HELIX 2 2 THR L 14B TYR L 14J 1 9 HELIX 3 3 ALA H 55 CYS H 58 5 4 HELIX 4 4 PRO H 60B ASP H 60E 5 4 HELIX 5 5 THR H 60I ASN H 62 5 3 HELIX 6 6 ASP H 125 LEU H 130 1 9 HELIX 7 7 GLU H 164 ASP H 170 1 7 HELIX 8 8 LYS H 185 GLY H 186C 5 5 HELIX 9 9 VAL H 231 ASP H 243 1 13 HELIX 10 10 PRO I 60 LEU I 64 5 5 SHEET 1 A 7 SER H 20 ASP H 21 0 SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 A 7 LYS H 135 GLY H 140 -1 N GLY H 136 O LEU H 160 SHEET 4 A 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 A 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 A 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 A 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 B 7 LYS H 81 SER H 83 0 SHEET 2 B 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 B 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 4 B 7 GLU H 39 LEU H 46 -1 O LEU H 41 N LEU H 33 SHEET 5 B 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 6 B 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 B 7 LEU H 85 ILE H 90 -1 N LYS H 87 O LYS H 107 SHEET 1 C 2 LEU H 60 TYR H 60A 0 SHEET 2 C 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.01 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.03 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.02 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.03 LINK C GLU I 62 N TYS I 63 1555 1555 1.31 LINK C TYS I 63 N LEU I 64 1555 1555 1.29 LINK O PHE H 204A CA CA H 392 1555 1555 2.43 LINK O ARG H 221A NA NA H 391 1555 1555 2.48 LINK O LYS H 224 NA NA H 391 1555 1555 2.48 LINK NA NA H 391 O HOH H 433 1555 1555 2.54 LINK NA NA H 391 O HOH H 431 1555 1555 2.59 LINK NA NA H 391 O HOH H 411 1555 1555 2.67 LINK NA NA H 391 O HOH H 414 1555 1555 2.96 LINK CA CA H 392 O HOH H 477 1555 1555 2.44 LINK CA CA H 392 O HOH H 484 1555 1555 2.40 LINK CA CA H 392 O HOH H 424 1555 1555 2.40 CISPEP 1 SER H 36A PRO H 37 0 -14.20 SITE 1 AC1 6 ARG H 221A LYS H 224 HOH H 411 HOH H 414 SITE 2 AC1 6 HOH H 431 HOH H 433 SITE 1 AC2 6 LYS H 169 THR H 172 PHE H 204A HOH H 424 SITE 2 AC2 6 HOH H 477 HOH H 484 SITE 1 AC3 14 LEU H 41 HIS H 57 CYS H 58 LYS H 60F SITE 2 AC3 14 ASP H 189 ALA H 190 GLU H 192 SER H 195 SITE 3 AC3 14 VAL H 213 GLY H 219 GLY H 226 HOH H 445 SITE 4 AC3 14 HOH H 475 HOH H 476 SITE 1 AC4 16 PHE H 34 LYS H 36 GLN H 38 LEU H 40 SITE 2 AC4 16 LEU H 65 ARG H 67 ARG H 73 THR H 74 SITE 3 AC4 16 ARG H 75 TYR H 76 LYS H 81 ILE H 82 SITE 4 AC4 16 MET H 84 HOH H 442 HOH H 487 HOH I 520 CRYST1 71.340 72.040 72.950 90.00 100.83 90.00 C 1 2 1 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 0.014017 0.000000 0.002682 0.00000 SCALE2 0.000000 0.013881 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013957 0.00000