PDB Short entry for 2CF9 HEADER HYDROLASE/HYDROLASE INHIBITOR 17-FEB-06 2CF9 TITLE COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: CATALYTIC, RESIDUES 364-620; COMPND 5 EC: 3.4.21.5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HIRUDIN IIIA; COMPND 9 CHAIN: I; COMPND 10 FRAGMENT: C-TERMINUS, RESIDUES 55-65; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 14 CHAIN: L; COMPND 15 FRAGMENT: LIGHT CHAIN, RESIDUES 334-361; COMPND 16 EC: 3.4.21.5; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: OVARY; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 11 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 12 ORGANISM_TAXID: 6421; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 19 EXPRESSION_SYSTEM_CELL_LINE: OVARY KEYWDS HYDROLASE/INHIBITOR, ACUTE PHASE, BLOOD COAGULATION, CALCIUM-BINDING, KEYWDS 2 GLYCOPROTEIN, HYDOLASE, SERINE PROTEASE, SERINE PROTEASE INHIBITOR KEYWDS 3 COMPLEX, COMPLEX HYDROLASE-INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.SCHWEIZER,A.HOFFMANN-ROEDER,J.A.OLSEN,U.OBST-SANDER,B.WAGNER, AUTHOR 2 M.KANSY,D.W.BANNER,F.DIEDERICH REVDAT 7 13-DEC-23 2CF9 1 REMARK LINK REVDAT 6 05-JUL-17 2CF9 1 REMARK REVDAT 5 29-MAR-17 2CF9 1 TITLE REVDAT 4 07-AUG-13 2CF9 1 REMARK REVDAT 3 13-JUL-11 2CF9 1 VERSN REVDAT 2 24-FEB-09 2CF9 1 VERSN REVDAT 1 14-JUN-06 2CF9 0 JRNL AUTH E.SCHWEIZER,A.HOFFMANN-ROEDER,J.A.OLSEN,P.SEILER, JRNL AUTH 2 U.OBST-SANDER,B.WAGNER,M.KANSY,D.W.BANNER,F.DIEDERICH JRNL TITL MULTIPOLAR INTERACTIONS IN THE D POCKET OF THROMBIN: LARGE JRNL TITL 2 DIFFERENCES BETWEEN TRICYCLIC IMIDE AND LACTAM INHIBITORS. JRNL REF ORG.BIOMOL.CHEM. V. 4 2364 2006 JRNL REFN ISSN 1477-0520 JRNL PMID 16763681 JRNL DOI 10.1039/B602585D REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 29702 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1582 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2053 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2301 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 494 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.44000 REMARK 3 B33 (A**2) : 0.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.80000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.636 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2398 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3242 ; 1.359 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 280 ; 6.117 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;32.102 ;23.482 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 420 ;11.608 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;12.718 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 338 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1822 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1040 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1580 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 341 ; 0.135 ; 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): 14 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.175 ; 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): 1412 ; 0.590 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2276 ; 1.035 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1039 ; 1.607 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 966 ; 2.498 ; 4.500 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 14 REMARK 3 ORIGIN FOR THE GROUP (A): 0.0440 10.8460 24.9190 REMARK 3 T TENSOR REMARK 3 T11: -0.0214 T22: -0.0431 REMARK 3 T33: -0.0143 T12: 0.0240 REMARK 3 T13: 0.0282 T23: -0.0160 REMARK 3 L TENSOR REMARK 3 L11: 1.5375 L22: 1.4550 REMARK 3 L33: 2.7459 L12: -0.5342 REMARK 3 L13: -0.2324 L23: -0.9498 REMARK 3 S TENSOR REMARK 3 S11: 0.0212 S12: -0.0020 S13: 0.0271 REMARK 3 S21: 0.0810 S22: -0.0424 S23: 0.0644 REMARK 3 S31: -0.1207 S32: -0.1523 S33: 0.0212 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 16 H 245 REMARK 3 ORIGIN FOR THE GROUP (A): 14.2570 -0.9050 20.0330 REMARK 3 T TENSOR REMARK 3 T11: -0.0357 T22: -0.0412 REMARK 3 T33: -0.0342 T12: 0.0165 REMARK 3 T13: 0.0032 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 1.1710 L22: 0.8758 REMARK 3 L33: 0.8150 L12: -0.5340 REMARK 3 L13: 0.1292 L23: -0.1270 REMARK 3 S TENSOR REMARK 3 S11: 0.0544 S12: 0.0483 S13: -0.0544 REMARK 3 S21: -0.0237 S22: -0.0412 S23: 0.0175 REMARK 3 S31: 0.0510 S32: 0.0489 S33: -0.0132 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : I 1 I 6 REMARK 3 ORIGIN FOR THE GROUP (A): 8.2550 -4.7990 -1.5640 REMARK 3 T TENSOR REMARK 3 T11: 0.0316 T22: 0.0485 REMARK 3 T33: 0.0301 T12: 0.1012 REMARK 3 T13: -0.0524 T23: -0.0620 REMARK 3 L TENSOR REMARK 3 L11: 4.7699 L22: 2.4474 REMARK 3 L33: 10.4653 L12: 3.1980 REMARK 3 L13: -1.7399 L23: 0.2875 REMARK 3 S TENSOR REMARK 3 S11: 0.1656 S12: 0.1400 S13: -0.1170 REMARK 3 S21: -1.0186 S22: -0.7449 S23: -0.4042 REMARK 3 S31: 0.9320 S32: 0.4581 S33: 0.5793 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: THE SIDE CHAIN OF ARG 75 HAS REMARK 3 ALTERNATIVE CONFORMATIONS, ONE OF WHICH IS ON A DIAD AXIS. IT REMARK 3 HAS NOT BEEN MODELLED. REMARK 4 REMARK 4 2CF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1290027821. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.40 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 : OSMIC MIRRORS REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31281 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 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 (%) : 91.4 REMARK 200 DATA REDUNDANCY : 4.540 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.13 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.400 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: PDB ENTRY 1OYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.40 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 35.64500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.92000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.64500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.92000 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.2 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 H2159 LIES ON A SPECIAL POSITION. REMARK 375 HOH H2385 LIES ON A SPECIAL POSITION. REMARK 375 HOH I2012 LIES ON A SPECIAL POSITION. REMARK 375 HOH L2064 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THROMBIN CLEAVES BONDS AFTER ARG AND LYS, CONVERTS FIBRINOGEN REMARK 400 TO FIBRIN AND ACTIVATES FACTORS V, VII, VIII, XIII REMARK 400 HIRUDIN IS A POTENT THROMBIN-SPECIFIC PROTEASE INHIBITOR 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 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 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 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 TYR H 60A 85.40 -152.04 REMARK 500 ASN H 60G 78.95 -155.23 REMARK 500 HIS H 71 -61.03 -129.38 REMARK 500 ILE H 79 -63.20 -127.68 REMARK 500 ASN H 95 76.60 -100.98 REMARK 500 GLU H 97A -84.35 -106.11 REMARK 500 SER H 214 -62.10 -109.66 REMARK 500 PHE L 7 -91.80 -127.99 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 H2025 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH H2028 DISTANCE = 8.83 ANGSTROMS REMARK 525 HOH H2029 DISTANCE = 9.93 ANGSTROMS REMARK 525 HOH H2032 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH H2033 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH H2035 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH H2042 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH H2058 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH H2061 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH H2117 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH H2135 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH H2179 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH L2072 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH L2073 DISTANCE = 6.43 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 H1249 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 89.3 89.6 REMARK 620 4 HOH H2288 O 118.1 125.4 139.5 REMARK 620 5 HOH H2291 O 76.1 145.8 76.5 81.7 REMARK 620 6 HOH H2302 O 65.9 74.3 153.3 65.6 105.1 REMARK 620 7 HOH H2347 O 163.9 92.1 85.2 74.9 117.0 116.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H1248 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 91.9 REMARK 620 3 HOH H2315 O 88.4 89.8 REMARK 620 4 HOH H2316 O 155.3 69.3 76.1 REMARK 620 5 HOH H2366 O 111.3 155.2 82.6 86.0 REMARK 620 6 HOH H2375 O 102.4 84.9 168.1 92.0 97.9 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 348 H 1247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 1248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 1249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN IIIA REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CF8 RELATED DB: PDB REMARK 900 THROMBIN-METHOXY DBREF 2CF9 H 16 245 UNP P00734 THRB_HUMAN 364 620 DBREF 2CF9 I 1 1 PDB 2CF9 2CF9 1 1 DBREF 2CF9 I 2 11 UNP P28508 ITHH_HIRME 56 65 DBREF 2CF9 L 1B 14L UNP P00734 THRB_HUMAN 334 361 SEQRES 1 H 257 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 257 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 257 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 257 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 257 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 257 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 257 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 257 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 257 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 257 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 257 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 257 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 257 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 257 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 257 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 257 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 257 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 257 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 257 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 257 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE SEQRES 1 I 11 SIN PHE GLU GLU ILE PRO GLU GLU TYR LEU GLN SEQRES 1 L 28 ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER SEQRES 2 L 28 LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR SEQRES 3 L 28 ILE ASP HET SIN I 1 7 HET 348 H1247 33 HET NA H1248 1 HET CA H1249 1 HETNAM SIN SUCCINIC ACID HETNAM 348 4-[(1R,3AS,4R,8AS,8BR)-1-ISOPROPYL-2-(4-METHOXYBENZYL)- HETNAM 2 348 3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4- HETNAM 3 348 YL]BENZENECARBOXIMIDAMIDE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION FORMUL 2 SIN C4 H6 O4 FORMUL 4 348 C27 H34 N4 O2 FORMUL 5 NA NA 1+ FORMUL 6 CA CA 2+ FORMUL 7 HOH *494(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 PHE H 245 1 12 HELIX 8 8 PHE L 7 SER L 11 5 5 HELIX 9 9 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 -1 O MET H 32 N ARG H 67 SHEET 4 HB 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 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-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS H 42 CYS H 58 1555 1555 2.02 SSBOND 2 CYS H 122 CYS L 1 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 2.07 LINK C4 SIN I 1 N PHE I 2 1555 1555 1.33 LINK O LYS H 169 CA CA H1249 1555 1555 2.72 LINK O THR H 172 CA CA H1249 1555 1555 2.67 LINK O PHE H 204A CA CA H1249 4546 1555 2.63 LINK O ARG H 221A NA NA H1248 1555 1555 2.25 LINK O LYS H 224 NA NA H1248 1555 1555 2.50 LINK NA NA H1248 O HOH H2315 1555 1555 2.92 LINK NA NA H1248 O HOH H2316 1555 1555 2.68 LINK NA NA H1248 O HOH H2366 1555 1555 2.39 LINK NA NA H1248 O HOH H2375 1555 1555 2.17 LINK CA CA H1249 O HOH H2288 1555 1555 3.13 LINK CA CA H1249 O HOH H2291 1555 1555 2.73 LINK CA CA H1249 O HOH H2302 1555 1555 2.87 LINK CA CA H1249 O HOH H2347 1555 4546 2.59 CISPEP 1 SER H 36A PRO H 37 0 -9.16 SITE 1 AC1 14 HIS H 57 TYR H 60A ASN H 98 LEU H 99 SITE 2 AC1 14 ASP H 189 ALA H 190 SER H 214 TRP H 215 SITE 3 AC1 14 GLY H 216 GLY H 219 GLY H 226 HOH H2206 SITE 4 AC1 14 HOH H2378 HOH H2400 SITE 1 AC2 6 ARG H 221A LYS H 224 HOH H2315 HOH H2316 SITE 2 AC2 6 HOH H2366 HOH H2375 SITE 1 AC3 6 LYS H 169 THR H 172 PHE H 204A HOH H2291 SITE 2 AC3 6 HOH H2302 HOH H2347 SITE 1 AC4 20 PHE H 34 GLN H 38 LEU H 65 ARG H 73 SITE 2 AC4 20 THR H 74 ARG H 75 TYR H 76 HOH H2142 SITE 3 AC4 20 HOH H2155 HOH H2268 HOH I2001 HOH I2002 SITE 4 AC4 20 HOH I2003 HOH I2004 HOH I2005 HOH I2006 SITE 5 AC4 20 HOH I2007 HOH I2008 HOH I2009 HOH I2011 CRYST1 71.290 71.840 73.060 90.00 100.56 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 0.014027 0.000000 0.002615 0.00000 SCALE2 0.000000 0.013920 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013923 0.00000