HEADER HYDROLASE/HYDROLASE INHIBITOR 01-FEB-01 1H8D TITLE X-RAY STRUCTURE OF THE HUMAN ALPHA-THROMBIN COMPLEX WITH A TRIPEPTIDE TITLE 2 PHOSPHONATE INHIBITOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: THROMBIN HEAVY CHAIN; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HIRUDIN I; COMPND 9 CHAIN: I; COMPND 10 FRAGMENT: RESIDUES 55 TO 64; COMPND 11 SYNONYM: LEPIRUDIN; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: THROMBIN; COMPND 14 CHAIN: L; COMPND 15 FRAGMENT: THROMBIN LIGHT CHAIN; COMPND 16 SYNONYM: COAGULATION FACTOR II; COMPND 17 EC: 3.4.21.5 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: HIRUDO MEDICINALIS; SOURCE 7 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 8 ORGANISM_TAXID: 6421; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS SERINE PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.SKORDALAKES,G.G.DODSON,D.GREEN,J.DEADMAN REVDAT 7 13-DEC-23 1H8D 1 SSBOND REVDAT 6 21-NOV-18 1H8D 1 REMARK LINK REVDAT 5 12-JUL-17 1H8D 1 REVDAT 4 13-JUL-11 1H8D 1 VERSN REVDAT 3 24-FEB-09 1H8D 1 VERSN REVDAT 2 16-AUG-01 1H8D 1 REVDAT JRNL REMARK SSBOND REVDAT 2 2 1 LINK HETATM CONECT MASTER REVDAT 1 26-FEB-01 1H8D 0 JRNL AUTH E.SKORDALAKES,G.G.DODSON,D.S.GREEN,C.A.GOODWIN,M.F.SCULLY, JRNL AUTH 2 H.R.HUDSON,V.V.KAKKAR,J.J.DEADMAN JRNL TITL INHIBITION OF HUMAN ALPHA-THROMBIN BY A PHOSPHONATE JRNL TITL 2 TRIPEPTIDE PROCEEDS VIA A METASTABLE PENTACOORDINATED JRNL TITL 3 PHOSPHORUS INTERMEDIATE JRNL REF J.MOL.BIOL. V. 311 549 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11493008 JRNL DOI 10.1006/JMBI.2001.4872 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.BERTRAND,J.OLEKSYSZYN,C.M.KAM,B.BODUSZEK,S.PRESNELL, REMARK 1 AUTH 2 R.R.PLASKON,F.L.SUDDATH,J.C.POWERS,L.D.WILLIAMS REMARK 1 TITL INHIBITION OF TRYPSIN AND THROMBIN BY AMINO REMARK 1 TITL 2 (4-AMIDINOPHENYL)METHANEPHOSPHONATE DIPHENYL ESTER REMARK 1 TITL 3 DERIVATIVES: X-RAY AND MOLECULAR MODELS REMARK 1 REF BIOCHEMISTRY V. 35 3147 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 8605148 REMARK 1 DOI 10.1021/BI9520996 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 68615 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2349 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 684 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.008 ; NULL REMARK 3 ANGLE DISTANCE (A) : 1.200 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1H8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1290005851. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX7.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.48800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68615 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14200 REMARK 200 R SYM FOR SHELL (I) : 0.13100 REMARK 200 FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1HGT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8K, 0.05MM NAHPO4, 0.1M NACL, REMARK 280 PH 7.20 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 35.32000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.32000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.80000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, I, L 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 477 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 505 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 792 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 843 LIES ON A SPECIAL POSITION. REMARK 375 HOH I 129 LIES ON A SPECIAL POSITION. 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 CD NE CZ NH1 NH2 REMARK 470 LYS H 236 CD CE NZ REMARK 470 CYS H 259 N CA C O CB REMARK 470 SER H 261 N CA C O CB REMARK 470 SER H 262 N CA C O CB REMARK 470 VAL H 263 N CA C O CB CG1 REMARK 470 LEU H 264 N CA C O CB CG CD1 REMARK 470 ILE H 265 N CA C O CB CG1 CG2 REMARK 470 VAL H 266 N CA C O CB CG1 REMARK 470 VAL H 267 N CA C O CB CG1 REMARK 470 CYS H 268 N CA C O CB REMARK 470 GLU L 1A CG CD OE1 OE2 REMARK 470 ASP L 1C OD1 OD2 REMARK 470 CYS L 1 N REMARK 470 SER L 14L N CA C O CB 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 CG1 ILE H 90 CD1 ILE H 265 0.71 REMARK 500 CG LEU H 85 CD2 LEU H 264 0.80 REMARK 500 NZ LYS L 9 O HOH L 101 1.24 REMARK 500 CB SER L 11 OG SER L 14L 1.48 REMARK 500 CB VAL H 66 CG2 VAL H 263 1.48 REMARK 500 CB SER H 27 OG SER H 261 1.48 REMARK 500 CB VAL H 138 CG2 VAL H 266 1.49 REMARK 500 CB VAL H 157 CG2 VAL H 267 1.49 REMARK 500 CB SER H 72 OG SER H 262 1.49 REMARK 500 CB ILE H 90 CD1 ILE H 265 1.50 REMARK 500 CB LEU H 85 CD2 LEU H 264 1.50 REMARK 500 O ILE L 14K O HOH L 102 1.54 REMARK 500 CD1 LEU H 85 CD2 LEU H 264 1.72 REMARK 500 CB CYS H 42 SG CYS H 259 1.73 REMARK 500 SD MET H 180 O HOH H 737 1.75 REMARK 500 C54 PHW H 301 O HOH H 425 1.79 REMARK 500 C52 PHW H 301 O HOH H 722 1.80 REMARK 500 O HOH L 114 O HOH L 142 1.82 REMARK 500 O HOH H 465 O HOH H 877 1.83 REMARK 500 O HOH L 148 O HOH L 171 1.88 REMARK 500 OE1 GLU L 13 O HOH L 103 1.88 REMARK 500 O HOH I 112 O HOH I 121 1.88 REMARK 500 SD MET H 84 O HOH I 122 1.94 REMARK 500 CG1 VAL H 66 CG2 VAL H 263 1.97 REMARK 500 O HOH L 152 O HOH L 153 1.97 REMARK 500 O HOH H 591 O HOH H 846 1.99 REMARK 500 O HOH H 836 O HOH H 896 2.00 REMARK 500 O HOH H 781 O HOH H 842 2.00 REMARK 500 N THR H 177 CE MET H 180 2.01 REMARK 500 O HOH H 480 O HOH H 644 2.02 REMARK 500 O HOH H 453 O HOH H 487 2.02 REMARK 500 NZ LYS H 87 O HOH H 401 2.03 REMARK 500 O HOH H 656 O HOH H 797 2.04 REMARK 500 O HOH H 919 O HOH H 950 2.04 REMARK 500 O HOH H 917 O HOH H 958 2.04 REMARK 500 CG LYS H 236 O HOH H 912 2.05 REMARK 500 O LEU I 10 O HOH I 101 2.05 REMARK 500 O HOH H 805 O HOH H 925 2.06 REMARK 500 O HOH H 674 O HOH H 779 2.06 REMARK 500 O ILE L 14K O HOH L 104 2.06 REMARK 500 O HOH H 640 O HOH H 767 2.06 REMARK 500 O HOH H 488 O HOH H 859 2.08 REMARK 500 O HOH H 919 O HOH H 939 2.08 REMARK 500 C53 PHW H 301 O HOH H 722 2.09 REMARK 500 NE ARG H 97 O HOH H 402 2.09 REMARK 500 CG ARG H 50 O HOH H 590 2.09 REMARK 500 CG GLU I 4 O HOH I 113 2.09 REMARK 500 OE1 GLN H 151 O HOH H 403 2.09 REMARK 500 O HOH H 570 O HOH H 783 2.09 REMARK 500 O HOH H 671 O HOH H 791 2.10 REMARK 500 REMARK 500 THIS ENTRY HAS 77 CLOSE CONTACTS 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 O HOH H 754 O HOH H 754 2556 1.46 REMARK 500 O HOH H 520 O HOH H 634 3545 1.84 REMARK 500 O HOH H 931 O HOH H 944 3455 1.85 REMARK 500 O HOH H 801 O HOH H 801 2555 2.01 REMARK 500 O HOH H 658 O HOH H 759 4546 2.17 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 CYS L 1 CA CYS L 1 CB 0.542 REMARK 500 CYS L 1 CA CYS L 1 C 1.155 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 CYS H 42 CA - CB - SG ANGL. DEV. = 18.2 DEGREES REMARK 500 ARG H 97 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET H 106 CA - CB - CG ANGL. DEV. = 11.9 DEGREES REMARK 500 ARG H 137 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 CYS L 1 CB - CA - C ANGL. DEV. = -49.5 DEGREES REMARK 500 CYS L 1 CA - CB - SG ANGL. DEV. = 22.3 DEGREES REMARK 500 ARG L 4 NE - CZ - NH1 ANGL. DEV. = 3.4 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 H 36A 119.48 -165.87 REMARK 500 TYR H 60A 85.90 -151.61 REMARK 500 ASN H 60G 86.49 -160.33 REMARK 500 HIS H 71 -61.82 -132.27 REMARK 500 ILE H 79 -61.30 -129.75 REMARK 500 GLU H 97A -71.05 -118.12 REMARK 500 PHE L 7 -84.97 -130.64 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 951 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH H 952 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH H 953 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH H 954 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH H 955 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH H 956 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH H 957 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH H 958 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH H 959 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH H 960 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH H 961 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH H 962 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH H 963 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH H 964 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH H 965 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH H 966 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH H 967 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH H 968 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH H 969 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH H 970 DISTANCE = 7.10 ANGSTROMS REMARK 525 HOH H 971 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH H 972 DISTANCE = 7.84 ANGSTROMS REMARK 525 HOH I 134 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH I 135 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH I 136 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH I 137 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH I 138 DISTANCE = 7.37 ANGSTROMS REMARK 525 HOH L 174 DISTANCE = 6.18 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PHW H 301 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: N-[(BENZYLOXY)CARBONYL]-BETA-PHENYL-D-PHENYLALANYL- REMARK 630 N-{(1S,3E)-1-[DIHYDROXY(DIPHENOXY)-LAMBDA~5~-PHOSPHANYL]-4- REMARK 630 METHOXYBUT-3-EN-1-YL}-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 PHW H 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ 00O PRO 02E REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PHW K 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN I REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A2C RELATED DB: PDB REMARK 900 STRUCTURE OF THROMBIN INHIBITED BY AERUGINOSIN298-A FROM A BLUE- REMARK 900 GREEN ALGA REMARK 900 RELATED ID: 1A3B RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN ALPHA-THROMBIN WITH THE BIFUNCTIONAL BORONATE REMARK 900 INHIBITOR BOROLOG1 REMARK 900 RELATED ID: 1A3E RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN ALPHA-THROMBIN WITH THE BIFUNCTIONAL BORONATE REMARK 900 INHIBITOR BOROLOG2 REMARK 900 RELATED ID: 1A46 RELATED DB: PDB REMARK 900 THROMBIN COMPLEXED WITH HIRUGEN AND A BETA-STRAND MIMETIC INHIBITOR REMARK 900 RELATED ID: 1A4W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING INHIBITORS: REMARK 900 PROBES OF THE S1' BINDING SITE REMARK 900 RELATED ID: 1A5G RELATED DB: PDB REMARK 900 HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC REMARK 900 INHIBITOR AND HIRUGEN REMARK 900 RELATED ID: 1A61 RELATED DB: PDB REMARK 900 THROMBIN COMPLEXED WITH A BETA-MIMETIC THIAZOLE-CONTAINING INHIBITOR REMARK 900 RELATED ID: 1ABI RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH HIRULOG 3 REMARK 900 RELATED ID: 1ABJ RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE (PPACK) REMARK 900 WITH CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP REMARK 900 RELATED ID: 1AD8 RELATED DB: PDB REMARK 900 COMPLEX OF THROMBIN WITH AND INHIBITOR CONTAINING A NOVEL P1 MOIETY REMARK 900 RELATED ID: 1AE8 RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN INHIBITION BY EOC-D-PHE-PRO-AZALYS-ONP REMARK 900 RELATED ID: 1AFE RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN INHIBITION BY CBZ-PRO-AZALYS-ONP REMARK 900 RELATED ID: 1AHT RELATED DB: PDB REMARK 900 RELATED ID: 1AI8 RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN TERNARY COMPLEX WITH THE EXOSITE INHIBITOR REMARK 900 HIRUGEN AND ACTIVE SITE INHIBITOR PHCH2OCO-D-DPA- PRO-BOROMPG REMARK 900 RELATED ID: 1AIX RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN TERNARY COMPLEX WITH EXOSITE INHIBITOR HIRUGEN REMARK 900 AND ACTIVE SITE INHIBITOR PHCH2OCO-D-DPA-PRO-BOROVAL REMARK 900 RELATED ID: 1AWF RELATED DB: PDB REMARK 900 NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT REMARK 900 RELATED ID: 1AWH RELATED DB: PDB REMARK 900 NOVEL COVALENT THROMBIN INHIBITOR FROM PLANT EXTRACT REMARK 900 RELATED ID: 1AY6 RELATED DB: PDB REMARK 900 THROMBIN INHIBITOR FROM THEONALLA, CYCLOTHEANAMIDE-BASED REMARK 900 MACROCYCLIC TRIPEPTIDE MOTIF REMARK 900 RELATED ID: 1B5G RELATED DB: PDB REMARK 900 HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC REMARK 900 INHIBITOR AND HIRUGEN REMARK 900 RELATED ID: 1B7X RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN ALPHA-THROMBIN Y225I MUTANT BOUND TO D- PHE-PRO- REMARK 900 ARG-CHLOROMETHYLKETONE REMARK 900 RELATED ID: 1BA8 RELATED DB: PDB REMARK 900 THROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES REMARK 900 RELATED ID: 1BB0 RELATED DB: PDB REMARK 900 THROMBIN INHIBITORS WITH RIGID TRIPEPTIDYL ALDEHYDES REMARK 900 RELATED ID: 1BCU RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND PROFLAVIN REMARK 900 RELATED ID: 1BHX RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE COMPLEX OF HUMAN ALPHA THROMBIN WITH THE REMARK 900 INHIBITOR SDZ 229-357 REMARK 900 RELATED ID: 1BMM RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN COMPLEXED WITH [S-(R,R)]-4- [(AMINOIMINO REMARK 900 METHYL)AMINO]-N-[[1-[3-HYDROXY-2-[(2- NAPHTHALENYLSULFONYL) AMINO]- REMARK 900 1-OXOPROPYL]-2-PYRROLIDINYL] METHYL]BUTANAMIDE (BMS-186282) REMARK 900 RELATED ID: 1BMN RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN COMPLEXED WITH [S-(R,R)]-1- (AMINOIMINO METHYL) REMARK 900 -N-[[1-[N-[(2-NAPHTHALENYLSULFONYL)-L- SERYL]-PYRROLIDINYL] METHYL]- REMARK 900 3-PIPERIDENECARBOXAMIDE (BMS- 189090) REMARK 900 RELATED ID: 1BTH RELATED DB: PDB REMARK 900 STRUCTURE OF THROMBIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN REMARK 900 INHIBITOR REMARK 900 RELATED ID: 1C1U RELATED DB: PDB REMARK 900 RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE REMARK 900 PROTEASES REMARK 900 RELATED ID: 1C1V RELATED DB: PDB REMARK 900 RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE REMARK 900 PROTEASES REMARK 900 RELATED ID: 1C1W RELATED DB: PDB REMARK 900 RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE REMARK 900 PROTEASES REMARK 900 RELATED ID: 1C4U RELATED DB: PDB REMARK 900 SELECTIVE NON ELECTROPHILIC THROMBIN INHIBITORS WITH CYCLOHEXYL REMARK 900 MOIETIES. REMARK 900 RELATED ID: 1C4V RELATED DB: PDB REMARK 900 SELECTIVE NON ELECTROPHILIC THROMBIN INHIBITORS WITH CYCLOHEXYL REMARK 900 MOIETIES. REMARK 900 RELATED ID: 1C4Y RELATED DB: PDB REMARK 900 SELECTIVE NON-ELECTROPHILIC THROMBIN INHIBITORS REMARK 900 RELATED ID: 1C5L RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1- BINDING, REMARK 900 SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1C5N RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1- BINDING, REMARK 900 SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1C5O RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1- BINDING, REMARK 900 SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR REMARK 900 RELATED ID: 1CA8 RELATED DB: PDB REMARK 900 THROMBIN INHIBITORS WITH RIGID TRIPEPTIDYL ALDEHYDES REMARK 900 RELATED ID: 1D3D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH REMARK 900 BENZOTHIOPHENE INHIBITOR 4 REMARK 900 RELATED ID: 1D3P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN APLHA-THROMBIN IN COMPLEX WITH BENZO[B] REMARK 900 THIOPHENE INHIBITOR 3 REMARK 900 RELATED ID: 1D3Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B] REMARK 900 THIOPHENE INHIBITOR 2 REMARK 900 RELATED ID: 1D3T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZO[B] REMARK 900 THIOPHENE INHIBITOR 1 REMARK 900 RELATED ID: 1D4P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH 5- REMARK 900 AMIDINOINDOLE-4-BENZYLPIPERIDINE INHIBITOR REMARK 900 RELATED ID: 1D6W RELATED DB: PDB REMARK 900 STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON- ELECTROPHILIC REMARK 900 INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1 REMARK 900 RELATED ID: 1D9I RELATED DB: PDB REMARK 900 STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON- ELECTOPHILIC REMARK 900 INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1 REMARK 900 RELATED ID: 1DE7 RELATED DB: PDB REMARK 900 INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA- THROMBIN: REMARK 900 CRYSTAL STRUCTURE OF THE ENZYME-SUBSTRATE COMPLEX REMARK 900 RELATED ID: 1DIT RELATED DB: PDB REMARK 900 COMPLEX OF A DIVALENT INHIBITOR WITH THROMBIN REMARK 900 RELATED ID: 1DM4 RELATED DB: PDB REMARK 900 SER195ALA MUTANT OF HUMAN THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A REMARK 900 RELATED ID: 1DWB RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH (DES-AMINO ASP55) HIRUDIN (RESIDUES 55 - REMARK 900 65) AND BENZAMIDINE REMARK 900 RELATED ID: 1DWC RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH (DES-AMINO ASP55) HIRUDIN (RESIDUES 55 - REMARK 900 65) AND MD-805 (ARGATROBAN) REMARK 900 RELATED ID: 1DWD RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH (DES-AMINO ASP55) HIRUDIN (RESIDUES 55 - REMARK 900 65) AND NAPAP REMARK 900 RELATED ID: 1DWE RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH (DES-AMINO ASP55) HIRUDIN (RESIDUES 55 - REMARK 900 65) AND D-PHE-PRO-ARG-CHLOROMETHYLKETONE (PPACK) WITH REMARK 900 CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP REMARK 900 RELATED ID: 1DX5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE THROMBIN-THROMBOMODULIN COMPLEX REMARK 900 RELATED ID: 1E0F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN ALPHA-THROMBIN-HAEMADIN COMPLEX: AN REMARK 900 EXOSITE II-BINDING INHIBITOR REMARK 900 RELATED ID: 1EOJ RELATED DB: PDB REMARK 900 DESIGN OF P1' AND P3' RESIDUES OF TRIVALENT THROMBIN INHIBITORS AND REMARK 900 THEIR CRYSTAL STRUCTURES REMARK 900 RELATED ID: 1EOL RELATED DB: PDB REMARK 900 DESIGN OF P1' AND P3' RESIDUES OF TRIVALENT THROMBIN INHIBITORS AND REMARK 900 THEIR CRYSTAL STRUCTURES REMARK 900 RELATED ID: 1FPC RELATED DB: PDB REMARK 900 ALPHA-THROMBIN TERNARY COMPLEX WITH EXOSITE INHIBITOR HIRUGEN AND REMARK 900 ACTIVE SITE INHIBITOR DANSYLARGININE N-(3-ETHYL -1,5-PENTANE DIYL) REMARK 900 AMIDE (DAPA) REMARK 900 RELATED ID: 1FPH RELATED DB: PDB REMARK 900 ALPHA-THROMBIN TERNARY COMPLEX WITH HIRUDIN AND FIBRINOPEPTIDE A REMARK 900 RELATED ID: 1HAG RELATED DB: PDB REMARK 900 PRETHROMBIN2 COMPLEXED WITH HIRUGEN (N-ACETYLHIRUDIN 53 - 64 WITH REMARK 900 SULFATO-TYR 63) REMARK 900 RELATED ID: 1HAH RELATED DB: PDB REMARK 900 ALPHA THROMBIN COMPLEXED WITH HIRUGEN (N-ACETYLHIRUDIN 53 - 64 WITH REMARK 900 SULFATO-TYR 63) REMARK 900 RELATED ID: 1HAI RELATED DB: PDB REMARK 900 ALPHA THROMBIN COMPLEXED WITH D-PHE-PRO-ARG- CHLOROMETHYLKETONE REMARK 900 (PPACK) WITH CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP REMARK 900 RELATED ID: 1HAO RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE REMARK 900 GGTTGGTGTGGTTGG (BASED ON NMR MODEL OF DEOXYRIBONUCLEIC ACID) REMARK 900 RELATED ID: 1HAP RELATED DB: PDB REMARK 900 COMPLEX OF HUMAN ALPHA-THROMBIN WITH A 15MER OLIGONUCLEOTIDE REMARK 900 GGTTGGTGTGGTTGG (BASED ON X-RAY MODEL OF DEOXYRIBONUCLEIC ACID) REMARK 900 RELATED ID: 1HBT RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN COMPLEXED WITH A PEPTIDYL PYRIDINIUM METHYL REMARK 900 KETONE CONTAINING BIVALENT INHIBITOR REMARK 900 RELATED ID: 1HDT RELATED DB: PDB REMARK 900 RELATED ID: 1HGT RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH HIRUGEN REMARK 900 RELATED ID: 1HLT RELATED DB: PDB REMARK 900 ALPHA THROMBIN COMPLEXED WITH THROMBOMODULIN (NONDECAPEPTIDE) AND D- REMARK 900 PHE-PRO-ARG-CHLOROMETHYLKETONE (PPACK) WITH CHLOROMETHYLKETONE REMARK 900 REPLACED BY A METHYLENE GROUP REMARK 900 RELATED ID: 1HUT RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEXED WITH DEOXYRIBONUCLEIC ACID (5'-D REMARK 900 (GPGPTPTPGPGPTPGPTPGPGPTPTPGPG)-3') AND D-PHE-PRO-ARG- REMARK 900 CHLOROMETHYLKETONE (PPACK) WITH CHLOROMETHYLKETONE REPLACED BY A REMARK 900 METHYLENE GROUP REMARK 900 RELATED ID: 1HXE RELATED DB: PDB REMARK 900 SERINE PROTEASE REMARK 900 RELATED ID: 1HXF RELATED DB: PDB REMARK 900 HUMAN THROMBIN COMPLEX WITH HIRUDIN VARIANT REMARK 900 RELATED ID: 1IHS RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH HIRUTONIN-2 REMARK 900 RELATED ID: 1IHT RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH HIRUTONIN-6 REMARK 900 RELATED ID: 1LHC RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BOROARG-OH REMARK 900 RELATED ID: 1LHD RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BOROLYS-OH REMARK 900 RELATED ID: 1LHE RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BORO-N- BUTYL- REMARK 900 AMIDINO-GLYCINE-OH REMARK 900 RELATED ID: 1LHF RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO-BORO- HOMOLYS-OH REMARK 900 RELATED ID: 1LHG RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN COMPLEXED WITH AC-(D)PHE-PRO- BOROORNITHINE-OH REMARK 900 RELATED ID: 1NRN RELATED DB: PDB REMARK 900 ALPHA-THROMBIN NON-COVALENTLY COMPLEXED WITH RECEPTOR BASED PEPTIDE REMARK 900 NRS REMARK 900 RELATED ID: 1NRO RELATED DB: PDB REMARK 900 ALPHA-THROMBIN NON-COVALENTLY COMPLEXED WITH RECEPTOR BASED PEPTIDE REMARK 900 NRP REMARK 900 RELATED ID: 1NRP RELATED DB: PDB REMARK 900 ALPHA-THROMBIN NON-COVALENTLY COMPLEXED WITH RECEPTOR BASED PEPTIDE REMARK 900 NR'S REMARK 900 RELATED ID: 1NRQ RELATED DB: PDB REMARK 900 ALPHA-THROMBIN NON-COVALENTLY COMPLEXED WITH RECEPTOR BASED PEPTIDE REMARK 900 D-FPR'S REMARK 900 RELATED ID: 1NRR RELATED DB: PDB REMARK 900 ALPHA-THROMBIN NON-COVALENTLY COMPLEXED WITH RECEPTOR BASED PEPTIDE REMARK 900 XA AND D-PHE-PRO-ARG CHLOROMETHYLKETONE (PPACK) WITH REMARK 900 CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP REMARK 900 RELATED ID: 1NRS RELATED DB: PDB REMARK 900 ALPHA-THROMBIN NON-COVALENTLY COMPLEXED WITH RECEPTOR BASED PEPTIDE REMARK 900 NRP (CLEAVED, FIRST FOUR RESIDUES ONLY) AND HIRUGEN REMARK 900 RELATED ID: 1PPB RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH D-PHE-PRO-ARG CHLOROMETHYLKETONE (PPACK) REMARK 900 WITH CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP REMARK 900 RELATED ID: 1QBV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THROMBIN COMPLEXED WITH AN GUANIDINE- MIMETIC REMARK 900 INHIBITOR REMARK 900 RELATED ID: 1QHR RELATED DB: PDB REMARK 900 NOVEL COVALENT ACTIVE SITE THROMBIN INHIBITORS REMARK 900 RELATED ID: 1QJ1 RELATED DB: PDB REMARK 900 NOVEL COVALENT ACTIVE SITE THROMBIN INHIBITORS REMARK 900 RELATED ID: 1QJ6 RELATED DB: PDB REMARK 900 NOVEL COVALENT ACTIVE SITE THROMBIN INHIBITORS REMARK 900 RELATED ID: 1QJ7 RELATED DB: PDB REMARK 900 NOVEL COVALENT ACTIVE SITE THROMBIN INHIBITORS REMARK 900 RELATED ID: 1QUR RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN IN COMPLEX WITH BIVALENT, BENZAMIDINE- BASED REMARK 900 SYNTHETIC INHIBITOR REMARK 900 RELATED ID: 1TBZ RELATED DB: PDB REMARK 900 HUMAN THROMBIN WITH ACTIVE SITE N-METHYL-D-PHENYLALANYL-N- [5- REMARK 900 (AMINOIMINOMETHYL)AMINO]-1-{{BENZOTHIAZOLYL)CARBONYL] BUTYL]-L- REMARK 900 PROLINAMIDE TRIFLUROACETATE AND EXOSITE-HIRUGEN REMARK 900 RELATED ID: 1THP RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN ALPHA-THROMBIN Y225P MUTANT BOUND TO D- PHE-PRO- REMARK 900 ARG-CHLOROMETHYLKETONE REMARK 900 RELATED ID: 1THR RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH HIRULLIN REMARK 900 RELATED ID: 1THS RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH MDL-28050 REMARK 900 RELATED ID: 1TMB RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH HIRUGEN AND CYCLOTHEONAMIDE A REMARK 900 RELATED ID: 1TMT RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEXED WITH CGP 50,856 (D-PHE-PRO-ARG-PRO -GLY- REMARK 900 GLY-GLY-GLY FOLLOWED BY RESIDUES 53 - 65 OF HIRUDIN, CLEAVED AFTER REMARK 900 ARG I 3) REMARK 900 RELATED ID: 1TMU RELATED DB: PDB REMARK 900 ALPHA-THROMBIN TERNARY COMPLEX WITH HIRUDIN (C-TERMINAL FRAGMENT, REMARK 900 RESIDUES 55 - 65) AND PPACK (D-PHE-PRO-ARG- CHLOROMETHYLKETONE) REMARK 900 RELATED ID: 1TOM RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEXED WITH HIRUGEN REMARK 900 RELATED ID: 1UMA RELATED DB: PDB REMARK 900 ALPHA-THROMBIN (HIRUGEN) COMPLEXED WITH NA-(N,N- DIMETHYLCARBAMOYL) REMARK 900 -ALPHA-AZALYSINE REMARK 900 RELATED ID: 1UVS RELATED DB: PDB REMARK 900 BOVINE THROMBIN--BM51.1011 COMPLEX REMARK 900 RELATED ID: 1VR1 RELATED DB: PDB REMARK 900 SPECIFITY FOR PLASMINOGEN ACTIVATOR INHIBITOR-1 REMARK 900 RELATED ID: 2HGT RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH HIRULOG I (CLEAVED BETWEEN ARG 3 AND REMARK 900 PRO 4) REMARK 900 RELATED ID: 2HNT RELATED DB: PDB REMARK 900 GAMMA-THROMBIN REMARK 900 RELATED ID: 2HPP RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH D-PHE-PRO-ARG- CHLOROMETHYLKETONE REMARK 900 (PPACK) CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP AND BOVINE REMARK 900 PROTHROMBIN FRAGMENT 2 REMARK 900 RELATED ID: 2HPQ RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH D-PHE-PRO-ARG- CHLOROMETHYLKETONE REMARK 900 (PPACK) CHLOROMETHYLKETONE REPLACED BY A METHYLENE GROUP AND HUMAN REMARK 900 PROTHROMBIN FRAGMENT 2 REMARK 900 RELATED ID: 2THF RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN ALPHA-THROMBIN Y225F MUTANT BOUND TO D- PHE-PRO- REMARK 900 ARG-CHLOROMETHYLKETONE REMARK 900 RELATED ID: 3HAT RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEXED WITH HIRUGEN AND FPAM (FIBRINOPEPTIDE A REMARK 900 MIMIC) REMARK 900 RELATED ID: 3HTC RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH RECOMBINANT HIRUDIN (VARIANT 2, LYS47) REMARK 900 RELATED ID: 4HTC RELATED DB: PDB REMARK 900 ALPHA-THROMBIN COMPLEX WITH RECOMBINANT HIRUDIN (VARIANT 2, LYS47) REMARK 900 RELATED ID: 4THN RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF ALPHA-THROMBIN-HIRUNORM IV COMPLEX REVEALS REMARK 900 A NOVEL SPECIFICITY SITE RECOGNITION MODE. REMARK 900 RELATED ID: 5GDS RELATED DB: PDB REMARK 900 HIRUNORMS ARE TRUE HIRUDIN MIMETICS. THE CRYSTAL STRUCTURE OF HUMAN REMARK 900 ALPHA-THROMBIN:HIRUNORM V COMPLEX REMARK 900 RELATED ID: 7KME RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2711. REMARK 900 RELATED ID: 8KME RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN INHIBITED WITH SEL2770. DBREF 1H8D L 1 14L UNP P00734 THRB_HUMAN 333 361 DBREF 1H8D H 16 147 UNP P00734 THRB_HUMAN 364 510 DBREF 1H8D H 150 259 UNP P00734 THRB_HUMAN 518 622 DBREF 1H8D H 261 268 PDB 1H8D 1H8D 261 268 DBREF 1H8D I 1 10 UNP P01050 ITH1_HIRME 55 64 SEQRES 1 H 260 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 260 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 260 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 260 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 260 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 260 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 260 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 260 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 260 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 260 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 260 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 260 LEU LYS GLU THR GLY GLN PRO SER VAL LEU GLN VAL VAL SEQRES 13 H 260 ASN LEU PRO ILE VAL GLU ARG PRO VAL CYS LYS ASP SER SEQRES 14 H 260 THR ARG ILE ARG ILE THR ASP ASN MET PHE CYS ALA GLY SEQRES 15 H 260 TYR LYS PRO ASP GLU GLY LYS ARG GLY ASP ALA CYS GLU SEQRES 16 H 260 GLY ASP SER GLY GLY PRO PHE VAL MET LYS SER PRO PHE SEQRES 17 H 260 ASN ASN ARG TRP TYR GLN MET GLY ILE VAL SER TRP GLY SEQRES 18 H 260 GLU GLY CYS ASP ARG ASP GLY LYS TYR GLY PHE TYR THR SEQRES 19 H 260 HIS VAL PHE ARG LEU LYS LYS TRP ILE GLN LYS VAL ILE SEQRES 20 H 260 ASP GLN PHE GLY CYS SER SER VAL LEU ILE VAL VAL CYS SEQRES 1 I 10 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU SEQRES 1 L 29 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 L 29 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER SEQRES 3 L 29 TYR ILE SER MODRES 1H8D TYS I 9 TYR O-SULFO-L-TYROSINE HET TYS I 9 16 HET PHW H 301 53 HETNAM TYS O-SULFO-L-TYROSINE HETNAM PHW N-[(BENZYLOXY)CARBONYL]-BETA-PHENYL-D-PHENYLALANYL-N- HETNAM 2 PHW {(1S,3E)-1-[DIHYDROXY(DIPHENOXY)-LAMBDA~5~- HETNAM 3 PHW PHOSPHANYL]-4-METHOXYBUT-3-EN-1-YL}-L-PROLINAMIDE FORMUL 2 TYS C9 H11 N O6 S FORMUL 4 PHW C45 H48 N3 O9 P FORMUL 5 HOH *684(H2 O) HELIX 1 1 ALA H 55 CYS H 58 5 4 HELIX 2 2 PRO H 60B ASP H 60E 5 4 HELIX 3 3 THR H 60I ASN H 62 5 3 HELIX 4 4 ASP H 125 LEU H 130 1 9 HELIX 5 5 GLU H 164 SER H 171 1 8 HELIX 6 6 LYS H 185 GLY H 186C 5 5 HELIX 7 7 LEU H 234 GLY H 246 1 13 HELIX 8 8 PRO I 6 LEU I 10 5 5 HELIX 9 9 PHE L 7 SER L 11 5 5 HELIX 10 10 THR L 14B TYR L 14J 1 9 SHEET 1 HA 7 SER H 20 ASP H 21 0 SHEET 2 HA 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 HA 7 LYS H 135 GLY H 140 -1 O GLY H 136 N LEU H 160 SHEET 4 HA 7 PRO H 198 LYS H 202 -1 O PRO H 198 N THR H 139 SHEET 5 HA 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 HA 7 GLY H 226 HIS H 230 -1 O PHE H 227 N SER H 214 SHEET 7 HA 7 MET H 180 ALA H 183 -1 O PHE H 181 N TYR H 228 SHEET 1 HB 7 LYS H 81 SER H 83 0 SHEET 2 HB 7 LEU H 64 ILE H 68 -1 O VAL H 66 N SER H 83 SHEET 3 HB 7 GLN H 30 ARG H 35 0 SHEET 4 HB 7 GLU H 39 LEU H 46 0 SHEET 5 HB 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 6 HB 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 HB 7 LEU H 85 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 1 HC 2 LEU H 60 TYR H 60A 0 SHEET 2 HC 2 LYS H 60F ASN H 60G 0 SSBOND 1 CYS H 42 CYS H 58 1555 1555 2.04 SSBOND 2 CYS H 42 CYS H 259 1555 1555 2.31 SSBOND 3 CYS H 58 CYS H 259 1555 1555 2.37 SSBOND 4 CYS H 122 CYS L 1 1555 1555 2.04 SSBOND 5 CYS H 168 CYS H 182 1555 1555 2.07 SSBOND 6 CYS H 191 CYS H 220 1555 1555 2.06 LINK C GLU I 8 N TYS I 9 1555 1555 1.33 LINK C TYS I 9 N LEU I 10 1555 1555 1.33 CISPEP 1 SER H 36A PRO H 37 0 -0.79 SITE 1 AC1 23 HIS H 57 TYR H 60A TRP H 60D GLU H 97A SITE 2 AC1 23 GLU H 146 ALA H 190 CYS H 191 GLU H 192 SITE 3 AC1 23 SER H 195 TRP H 215 GLY H 216 GLU H 217 SITE 4 AC1 23 GLY H 219 CYS H 220 HOH H 449 HOH H 425 SITE 5 AC1 23 HOH H 476 HOH H 722 HOH H 423 HOH H 535 SITE 6 AC1 23 HOH H 445 HOH H 422 HOH H 579 SITE 1 AC2 33 PHE H 34 LEU H 65 ARG H 73 THR H 74 SITE 2 AC2 33 ARG H 75 TYR H 76 GLU H 80 LYS H 81 SITE 3 AC2 33 ILE H 82 SER H 262 HOH H 417 HOH H 470 SITE 4 AC2 33 HOH H 533 HOH H 516 HOH H 555 HOH H 471 SITE 5 AC2 33 HOH I 106 HOH I 117 HOH I 104 HOH I 116 SITE 6 AC2 33 HOH I 110 HOH I 107 HOH I 108 HOH I 115 SITE 7 AC2 33 HOH I 113 HOH I 103 HOH I 111 HOH I 112 SITE 8 AC2 33 HOH I 105 HOH I 102 HOH I 114 HOH I 109 SITE 9 AC2 33 HOH I 101 CRYST1 70.640 71.600 71.900 90.00 100.35 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 0.014156 0.000000 0.002585 0.00000 SCALE2 0.000000 0.013966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014138 0.00000