HEADER HYDROLASE/HYDROLASE INHIBITOR 07-APR-03 1OYT TITLE COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED FLUORINATED TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 9 CHAIN: H; COMPND 10 SYNONYM: COAGULATION FACTOR II; COMPND 11 EC: 3.4.21.5; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HIRUDIN IIB; 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 GENE: F2; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 EXPRESSION_SYSTEM_CELL: OVARY; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: F2; SOURCE 15 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 16 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 18 EXPRESSION_SYSTEM_CELL: OVARY; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 22 ORGANISM_TAXID: 6421; SOURCE 23 OTHER_DETAILS: THE SEQUENCE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 24 IS NATURALLY FOUND IN HIRUDO MEDICINALIS (MEDICINAL LEECH). KEYWDS SERINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.W.BANNER,J.A.OLSEN REVDAT 6 03-APR-24 1OYT 1 REMARK SEQADV LINK REVDAT 5 11-OCT-17 1OYT 1 REMARK REVDAT 4 25-MAY-16 1OYT 1 SOURCE REVDAT 3 13-JUL-11 1OYT 1 VERSN REVDAT 2 24-FEB-09 1OYT 1 VERSN REVDAT 1 24-JUN-03 1OYT 0 JRNL AUTH J.A.OLSEN,D.W.BANNER,P.SEILER,U.OBST-SANDER,A.D'ARCY, JRNL AUTH 2 M.STIHLE,K.MUELLER,F.DIEDERICH JRNL TITL A FLUORINE SCAN OF THROMBIN INHIBITORS TO MAP THE JRNL TITL 2 FLUOROPHILICITY/FLUOROPHOBICITY OF AN ENZYME ACTIVE SITE: JRNL TITL 3 EVIDENCE FOR CF...C=O INTERACTIONS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 42 2507 2003 JRNL REFN ISSN 1433-7851 JRNL PMID 12800172 JRNL DOI 10.1002/ANIE.200351268 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.RUSSO,A.GAST,E.J.SCHLAEGER,A.ANGIOLILLO,C.PIETROPAOLO REMARK 1 TITL STABLE EXPRESSION AND PURIFICATION OF A SECRETED HUMAN REMARK 1 TITL 2 RECOMBINANT PRETHROMBIN-2 AND ITS ACTIVATION TO THROMBIN REMARK 1 REF PROTEIN EXPR.PURIF. V. 10 214 1997 REMARK 1 REFN ISSN 1046-5928 REMARK 1 DOI 10.1006/PREP.1997.0733 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2000 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.30 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) (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 38750 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 BUT NOT SAME AS FOR REMARK 3 PREVIOUS REFINED STRUCTURES REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1938 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL 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 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.73 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3436 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 181 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2292 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 404 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : -1.35000 REMARK 3 B33 (A**2) : 0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.76000 REMARK 3 B23 (A**2) : 0.00000 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.060 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.630 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.090 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.470 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.140 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 48.77 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 : ROCHE.PARAM REMARK 3 PARAMETER FILE 3 : FSN.PRX REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ROCHE.TOP REMARK 3 TOPOLOGY FILE 3 : FSN.TPX REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS REMARK 3 USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE REMARK 3 STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8, REMARK 3 3467-3475). REMARK 3 DOUBLE CONFROMATIONS GIVEN AS SINGLE CONFORMER ARE: REMARK 3 H CHAIN LEU41, ARG50, LEU64, VAL66, LEU85, MET106, SER129B REMARK 3 LEU130, ASP186. REMARK 3 GLY186C HAS A SECOND TRACE WITH PSI OF 186D + 180DEGREES. REMARK 3 MISSING RESIDUES H CHAIN: 148 LOOP WTANVGK, REMARK 3 RESIDUES THR147 AND GLN151 WEAK. REMARK 3 MISSING RESIDUES L CHAIN: N-TERMINUS TFGSGE, C-TERMINUS DGR. REMARK 3 MISSING FROM 'HIRUGEN' I CHAIN: C-TERMINUS EEYLQ. REMARK 3 HIRUGEN CORRESPONDS TO HIRUDIN 55-65, IS SYNTHESIZED CHEMICALLY, REMARK 3 IS NOT REMARK 3 SULPHATED. ASP 55 HAS NO AMINO GROUP AND THUS IS GIVEN AS A REMARK 3 SUCCINIC ACID RESIDUE. REMARK 3 REMARK 3 ARG75 HAS 2 CONFORMATIONS. COORDINATES ARE GIVEN UP TO CB. REMARK 3 WATERS 107 AND 35 INDICATE THE GUANIDINIUM POSITION ON THE 2-FOLD REMARK 3 AXIS. REMARK 3 REMARK 3 RESIDUES WITH SOME OR ALL ATOMS AT 0.5 OCCUPANCY ARE REMARK 3 L CHAIN: ASP1A, LYS14A, ARG14D, ILE14K, REMARK 3 H CHAIN: LEU41, LYS81, LYS110, PRO111, ARG126, GLU127, SER129B, REMARK 3 THR147, GLN151, ASP186A, LYS186D, GLU192, ASN205, LYS236 REMARK 3 GLN239, LYS240, GLN244, REMARK 3 I CHAIN GLU4, PRO6. REMARK 3 REMARK 3 ATOMS WITH ZERO OCCUPANCY H CHAIN SER36A OG AND ASN62 OD1. REMARK 3 THE SUGAR ON ASN62 IS NOT MODELLED (WATER MOLECULES). REMARK 3 REMARK 3 ALL INHIBITOR ATOMS REFINE TO B-VALUES < 25. THE WEAKEST IS O18. REMARK 3 BETWEEN O18 AND THE NZ OF K60F IS A SMEAR OF DENSITY, NOT REMARK 3 WELL FITTED BY WATER 233. REMARK 4 REMARK 4 1OYT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMICS REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38758 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 200 DATA REDUNDANCY : 7.330 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : 0.04200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.4300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.25 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : 0.17000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.710 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: IN HOUSE THROMBIN STRUCTURES REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 35.34650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.73950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.34650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.73950 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: 4270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 780 LIES ON A SPECIAL POSITION. REMARK 375 HOH I 107 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE N-TERMINAL ASP DES-AMINO HIRUDIN-3A' IS OLIGOPEPTIDE, A MEMBER REMARK 400 OF ANTICOAGULANT, ANTITHROMBOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: N-TERMINAL ASP DES-AMINO HIRUDIN-3A' REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 THR L 1H REMARK 465 PHE L 1G REMARK 465 GLY L 1F REMARK 465 SER L 1E REMARK 465 GLY L 1D REMARK 465 GLU L 1C REMARK 465 ASP L 14L REMARK 465 GLY L 14M REMARK 465 ARG L 15 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 465 GLU I 7 REMARK 465 GLU I 8 REMARK 465 TYR I 9 REMARK 465 LEU I 10 REMARK 465 GLN I 11 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG H 75 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER H 36A OG REMARK 480 ASN H 62 OD1 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 PHE L 7 -89.39 -130.62 REMARK 500 TYR H 60A 85.28 -155.19 REMARK 500 ASN H 60G 83.20 -158.47 REMARK 500 HIS H 71 -59.91 -133.89 REMARK 500 ILE H 79 -62.21 -125.98 REMARK 500 GLU H 97A -73.52 -110.93 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 CA H 701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 72.7 REMARK 620 3 PHE H 204A O 92.3 92.4 REMARK 620 4 HOH H 743 O 160.6 89.4 80.6 REMARK 620 5 HOH H 761 O 62.3 70.6 152.3 119.6 REMARK 620 6 HOH H 791 O 78.3 149.1 78.0 117.3 105.2 REMARK 620 7 HOH H 868 O 119.3 124.6 135.8 76.9 70.8 79.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 601 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 92.1 REMARK 620 3 HOH H 724 O 158.6 69.2 REMARK 620 4 HOH H 727 O 110.5 157.1 87.9 REMARK 620 5 HOH H 729 O 90.8 90.9 79.6 85.4 REMARK 620 6 HOH H 737 O 99.3 82.8 89.0 96.5 168.3 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FSN H 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN IIB DBREF 1OYT L 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 1OYT H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 1OYT I 1 11 UNP P28506 ITHF_HIRME 55 65 SEQADV 1OYT SIN I 1 UNP P28506 ASP 55 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 SIN PHE GLU GLU ILE PRO GLU GLU TYR LEU GLN HET SIN I 1 7 HET NA H 601 1 HET CA H 701 1 HET FSN H 501 30 HETNAM SIN SUCCINIC ACID HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETNAM FSN (3ASR,4RS,8ASR,8BRS)-4-(2-(4-FLUOROBENZYL)-1,3- HETNAM 2 FSN DIOXODEACAHYDROPYRROLO[3,4-A] PYRROLIZIN-4-YL) HETNAM 3 FSN BENZAMIDINE FORMUL 3 SIN C4 H6 O4 FORMUL 4 NA NA 1+ FORMUL 5 CA CA 2+ FORMUL 6 FSN C23 H24 F N4 O2 1+ FORMUL 7 HOH *404(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 SER H 171 1 8 HELIX 8 8 LYS H 185 GLY H 186C 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 VAL H 138 O VAL H 158 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 VAL H 66 O SER H 83 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 2.04 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.03 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.01 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05 LINK C1 SIN I 1 N PHE I 2 1555 1555 1.33 LINK O LYS H 169 CA CA H 701 1555 1555 2.69 LINK O THR H 172 CA CA H 701 1555 1555 2.65 LINK O PHE H 204A CA CA H 701 4546 1555 2.60 LINK O ARG H 221A NA NA H 601 1555 1555 2.40 LINK O LYS H 224 NA NA H 601 1555 1555 2.46 LINK NA NA H 601 O HOH H 724 1555 1555 2.53 LINK NA NA H 601 O HOH H 727 1555 1555 2.37 LINK NA NA H 601 O HOH H 729 1555 1555 2.76 LINK NA NA H 601 O HOH H 737 1555 1555 2.29 LINK CA CA H 701 O HOH H 743 1555 1555 2.55 LINK CA CA H 701 O HOH H 761 1555 1555 2.90 LINK CA CA H 701 O HOH H 791 1555 1555 2.65 LINK CA CA H 701 O HOH H 868 1555 1555 3.03 CISPEP 1 SER H 36A PRO H 37 0 -0.40 SITE 1 AC1 6 ARG H 221A LYS H 224 HOH H 724 HOH H 727 SITE 2 AC1 6 HOH H 729 HOH H 737 SITE 1 AC2 7 LYS H 169 THR H 172 PHE H 204A HOH H 743 SITE 2 AC2 7 HOH H 761 HOH H 791 HOH H 868 SITE 1 AC3 15 HIS H 57 TYR H 60A TRP H 60D GLU H 97A SITE 2 AC3 15 ASN H 98 LEU H 99 ASP H 189 ALA H 190 SITE 3 AC3 15 SER H 214 TRP H 215 GLY H 216 GLY H 219 SITE 4 AC3 15 GLY H 226 HOH H 703 HOH H 842 SITE 1 AC4 15 PHE H 34 GLN H 38 LEU H 65 ARG H 73 SITE 2 AC4 15 THR H 74 ARG H 75 TYR H 76 HOH H 742 SITE 3 AC4 15 HOH H 806 HOH H 819 HOH H 995 HOH I 241 SITE 4 AC4 15 HOH I 313 HOH I 326 HOH I 369 CRYST1 70.693 71.479 72.802 90.00 100.53 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 0.014146 0.000000 0.002629 0.00000 SCALE2 0.000000 0.013990 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013971 0.00000