PDB Short entry for 2C8Z HEADER HYDROLASE/HYDROLASE INHIBITOR 08-DEC-05 2C8Z TITLE THROMBIN INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN, LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FRAGMENT ALPHA THROMBIN, RESIDUES 328-363; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: FRAGMENT ALPHA THROMBIN, RESIDUES 364-622; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HIRUDIN VARIANT-2; COMPND 13 CHAIN: I; COMPND 14 FRAGMENT: PEPTIDE FRAGMENT OF HIRUGEN, RESIDUES 61-72; COMPND 15 SYNONYM: HIRUGEN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD PLASMA; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 TISSUE: BLOOD PLASMA; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 13 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 14 ORGANISM_TAXID: 6421 KEYWDS PROTEASE, BLOOD COAGULATION, THROMBIN, GAMMA-CARBOXYGLUTAMIC ACID, KEYWDS 2 GLYCOPROTEIN, KRINGLE, SERINE PROTEASE, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.HOWARD,C.ABELL,W.BLAKEMORE,R.CARR,G.CHESSARI,M.CONGREVE,S.HOWARD, AUTHOR 2 H.JHOTI,C.W.MURRAY,L.C.A.SEAVERS,R.L.M.VAN MONTFORT REVDAT 6 13-DEC-23 2C8Z 1 REMARK LINK REVDAT 5 28-JUN-17 2C8Z 1 REMARK REVDAT 4 07-AUG-13 2C8Z 1 REMARK REVDAT 3 13-JUL-11 2C8Z 1 VERSN REVDAT 2 24-FEB-09 2C8Z 1 VERSN REVDAT 1 04-JUL-06 2C8Z 0 JRNL AUTH N.HOWARD,C.ABELL,W.BLAKEMORE,G.CHESSARI,M.CONGREVE,S.HOWARD, JRNL AUTH 2 H.JHOTI,C.W.MURRAY,L.C.A.SEAVERS,R.L.M.VAN MONTFORT JRNL TITL APPLICATION OF FRAGMENT SCREENING AND FRAGMENT LINKING TO JRNL TITL 2 THE DISCOVERY OF NOVEL THROMBIN INHIBITORS JRNL REF J.MED.CHEM. V. 49 1346 2006 JRNL REFN ISSN 0022-2623 JRNL PMID 16480269 JRNL DOI 10.1021/JM050850V REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019C REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 17374 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 REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 947 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1147 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2362 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 327 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.39000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : -1.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.41000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.249 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.214 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.162 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.246 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2434 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1732 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3285 ; 1.333 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4179 ; 0.857 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 6.779 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;34.851 ;23.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 433 ;14.628 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;19.572 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 337 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2665 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 503 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 470 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1910 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1154 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1294 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 82 ; 0.107 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 3 ; 0.141 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 52 ; 0.283 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.177 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1442 ; 0.058 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2324 ; 0.078 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 992 ; 0.080 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 961 ; 0.097 ; 7.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. ELECTRON DENSITY PEAK CLOSE TO PHE 181 B MODELLED AS REMARK 3 DMSO. OCCUPANCY OF SIDE CHAIN ARG 75 B SET TO 0.5 BECAUSE OF REMARK 3 DISORDER AT TWOFOLD AXIS REMARK 4 REMARK 4 2C8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1290026757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.30 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : CONFOCAL MULTILAYER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17595 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 33.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 1.960 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: IN-HOUSE SOFTWARE REMARK 200 STARTING MODEL: PDB ENTRY 1QJ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.30 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 34.46900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.82850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.46900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.82850 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: 4210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 CZ ARG B 75 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2096 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 PROTHROMBIN: CONVERTS FIBRINOGEN TO FIBRIN AND ACTIVATES REMARK 400 FACTORS V, VII, VIII, XIII, AND, IN COMPLEX WITH REMARK 400 THROMBOMODULIN. REMARK 400 HIRUDIN: IT IS A POTENT THROMBIN-SPECIFIC PROTEASE INHIBITOR. 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 A -7 REMARK 465 PHE A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 ASP A 15 REMARK 465 GLY A 16 REMARK 465 ARG A 17 REMARK 465 THR B 146A REMARK 465 TRP B 146B REMARK 465 THR B 146C REMARK 465 ALA B 146D REMARK 465 ASN B 146E REMARK 465 VAL B 147 REMARK 465 GLY B 148 REMARK 465 LYS B 149 REMARK 465 GLY I 54 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 GLN I 65 CA C O CB CG CD OE1 REMARK 470 GLN I 65 NE2 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 O THR B 172 O HOH B 2194 2.17 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 PHE A 7 -85.13 -130.31 REMARK 500 SER B 48 -162.63 -163.97 REMARK 500 ASN B 60G 84.03 -151.69 REMARK 500 HIS B 71 -62.38 -130.42 REMARK 500 ILE B 79 -61.48 -128.47 REMARK 500 GLU B 97A -76.68 -98.60 REMARK 500 SER B 214 -69.09 -107.48 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 A2013 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2015 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH B2007 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH B2061 DISTANCE = 5.88 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 NA B1248 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 221A O REMARK 620 2 LYS B 224 O 86.3 REMARK 620 3 HOH B2205 O 151.3 70.4 REMARK 620 4 HOH B2206 O 86.8 88.4 76.3 REMARK 620 5 HOH B2245 O 108.6 164.1 93.7 87.0 REMARK 620 6 HOH B2253 O 91.1 72.2 97.2 160.6 111.9 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS B 1249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2A B 1250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN VARIANT-2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C8W RELATED DB: PDB REMARK 900 THROMBIN INHIBITORS REMARK 900 RELATED ID: 2C8X RELATED DB: PDB REMARK 900 THROMBIN INHIBITORS REMARK 900 RELATED ID: 2C8Y RELATED DB: PDB REMARK 900 THROMBIN INHIBITORS REMARK 900 RELATED ID: 2C90 RELATED DB: PDB REMARK 900 THROMBIN INHIBITORS REMARK 900 RELATED ID: 2C93 RELATED DB: PDB REMARK 900 THROMBIN INHIBITORS DBREF 2C8Z A -7 17 UNP P00734 THRB_HUMAN 328 363 DBREF 2C8Z B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 2C8Z I 54 65 UNP P09945 ITH3_HIRME 61 72 SEQRES 1 A 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 A 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 A 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 I 12 GLY ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 2C8Z TYS I 63 TYR O-SULFO-L-TYROSINE HET TYS I 63 16 HET NA B1248 1 HET DMS B1249 4 HET C2A B1250 9 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM C2A 1-(3-CHLOROPHENYL)METHANAMINE HETSYN C2A INHIBITOR OF THROMBIN FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA NA 1+ FORMUL 5 DMS C2 H6 O S FORMUL 6 C2A C7 H8 CL N FORMUL 7 HOH *327(H2 O) HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 THR A 14B TYR A 14J 1 9 HELIX 3 3 ALA B 55 LEU B 59 5 5 HELIX 4 4 TYR B 60A ASP B 60E 5 5 HELIX 5 5 THR B 60I ASN B 62 5 3 HELIX 6 6 ASP B 125 LEU B 130 1 9 HELIX 7 7 GLU B 164 ASP B 170 1 7 HELIX 8 8 LEU B 234 GLY B 246 1 13 HELIX 9 9 PRO I 60 LEU I 64 5 5 SHEET 1 BA 7 SER B 20 ASP B 21 0 SHEET 2 BA 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 BA 7 LYS B 135 GLY B 140 -1 O GLY B 136 N LEU B 160 SHEET 4 BA 7 PRO B 198 LYS B 202 -1 O PRO B 198 N THR B 139 SHEET 5 BA 7 TRP B 207 TRP B 215 -1 O TYR B 208 N MET B 201 SHEET 6 BA 7 GLY B 226 HIS B 230 -1 O PHE B 227 N SER B 214 SHEET 7 BA 7 MET B 180 ALA B 183 -1 O PHE B 181 N TYR B 228 SHEET 1 BB 7 GLN B 30 ARG B 35 0 SHEET 2 BB 7 GLU B 39 LEU B 46 -1 O GLU B 39 N ARG B 35 SHEET 3 BB 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 4 BB 7 ALA B 104 LEU B 108 -1 O ALA B 104 N THR B 54 SHEET 5 BB 7 LYS B 81 ILE B 90 -1 N GLU B 86 O LYS B 107 SHEET 6 BB 7 LEU B 64 ILE B 68 -1 O LEU B 64 N LEU B 85 SHEET 7 BB 7 GLN B 30 ARG B 35 -1 O MET B 32 N ARG B 67 SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.05 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.01 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.01 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.04 LINK C GLU I 62 N TYS I 63 1555 1555 1.33 LINK C TYS I 63 N LEU I 64 1555 1555 1.34 LINK O ARG B 221A NA NA B1248 1555 1555 2.35 LINK O LYS B 224 NA NA B1248 1555 1555 2.39 LINK NA NA B1248 O HOH B2205 1555 1555 2.59 LINK NA NA B1248 O HOH B2206 1555 1555 2.96 LINK NA NA B1248 O HOH B2245 1555 1555 2.38 LINK NA NA B1248 O HOH B2253 1555 1555 2.25 CISPEP 1 SER B 37 PRO B 37A 0 -3.25 SITE 1 AC1 6 ARG B 221A LYS B 224 HOH B2205 HOH B2206 SITE 2 AC1 6 HOH B2245 HOH B2253 SITE 1 AC2 5 LEU B 130 ILE B 162 PHE B 181 HOH B2177 SITE 2 AC2 5 HOH B2272 SITE 1 AC3 10 ASP B 189 ALA B 190 CYS B 191 SER B 195 SITE 2 AC3 10 VAL B 213 TRP B 215 GLY B 219 GLY B 226 SITE 3 AC3 10 PHE B 227 HOH B2273 SITE 1 AC4 16 PHE B 34 GLN B 38 LEU B 65 ARG B 73 SITE 2 AC4 16 THR B 74 ARG B 75 TYR B 76 LYS B 81 SITE 3 AC4 16 ILE B 82 HOH B2104 HOH I2002 HOH I2003 SITE 4 AC4 16 HOH I2004 HOH I2006 HOH I2008 HOH I2009 CRYST1 68.938 71.657 71.839 90.00 100.10 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 0.014506 0.000000 0.002584 0.00000 SCALE2 0.000000 0.013955 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014139 0.00000