HEADER HYDROLASE/HYDROLASE INHIBITOR 17-MAY-06 2CN0 TITLE COMPLEX OF RECOMBINANT HUMAN THROMBIN WITH A DESIGNED INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN PRECURSOR; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: RESIDUES 364-620; COMPND 5 SYNONYM: COAGULATION FACTOR II, THROMBIN; COMPND 6 EC: 3.4.21.5; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HIRUDIN IIA; COMPND 10 CHAIN: I; COMPND 11 FRAGMENT: HIRUDIN C-TERMINUS, RESIDUES 56-65; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: ASP PHE GLU GLU ILE PRO GLU GLU TYR LEU GLN; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: PROTHROMBIN PRECURSOR; COMPND 16 CHAIN: L; COMPND 17 FRAGMENT: RESIDUES 334-361; COMPND 18 SYNONYM: COAGULATION FACTOR II, THROMBIN; COMPND 19 EC: 3.4.21.5; COMPND 20 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 ACUTE PHASE, BLOOD COAGULATION, CALCIUM-BINDING, GLYCOPROTEIN, KEYWDS 2 HYDROLASE, SERINE PROTEASE, SERINE PROTEASE INHIBITOR COMPLEX, KEYWDS 3 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.HOFFMANN-RODER,E.SCHWEIZER,J.EGGER,P.SEILER,U.OBST-SANDER,B.WAGNER, AUTHOR 2 M.KANSY,D.W.BANNER,F.DIEDERICH REVDAT 7 13-DEC-23 2CN0 1 REMARK LINK REVDAT 6 29-MAR-17 2CN0 1 TITLE SOURCE REVDAT 5 07-AUG-13 2CN0 1 REMARK REVDAT 4 13-JUL-11 2CN0 1 VERSN REVDAT 3 24-FEB-09 2CN0 1 VERSN REVDAT 2 03-JAN-07 2CN0 1 MASTER REVDAT 1 06-NOV-06 2CN0 0 JRNL AUTH A.HOFFMANN-RODER,E.SCHWEIZER,J.EGGER,P.SEILER,U.OBST-SANDER, JRNL AUTH 2 B.WAGNER,M.KANSY,D.W.BANNER,F.DIEDERICH JRNL TITL MAPPING THE FLUOROPHILICITY OF A HYDROPHOBIC POCKET: JRNL TITL 2 SYNTHESIS AND BIOLOGICAL EVALUATION OF TRICYCLIC THROMBIN JRNL TITL 3 INHIBITORS DIRECTING FLUORINATED ALKYL GROUPS INTO THE P JRNL TITL 4 POCKET JRNL REF CHEMMEDCHEM V. 1 1205 2006 JRNL REFN ISSN 1860-7179 JRNL PMID 17001711 JRNL DOI 10.1002/CMDC.200600124 REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 79708 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4196 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6112 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 312 REMARK 3 BIN FREE R VALUE : 0.2600 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 : 34 REMARK 3 SOLVENT ATOMS : 397 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) : 20.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : -0.83000 REMARK 3 B33 (A**2) : 0.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.84000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.794 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2462 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2224 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3339 ; 1.597 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5187 ; 0.826 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 294 ; 5.862 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 113 ;32.331 ;23.363 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 435 ;12.191 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.312 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 349 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2717 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 519 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 429 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2383 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1194 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1529 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 273 ; 0.141 ; 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): 2 ; 0.083 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 30 ; 0.304 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.160 ; 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): 1455 ; 0.812 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2355 ; 1.363 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1053 ; 1.858 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 984 ; 2.671 ; 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): -0.1040 10.6950 24.5030 REMARK 3 T TENSOR REMARK 3 T11: -0.1264 T22: -0.0916 REMARK 3 T33: -0.1108 T12: 0.0386 REMARK 3 T13: 0.0432 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.5434 L22: 2.0119 REMARK 3 L33: 3.2188 L12: -0.6310 REMARK 3 L13: 0.3407 L23: -1.2910 REMARK 3 S TENSOR REMARK 3 S11: 0.0300 S12: -0.0767 S13: -0.0027 REMARK 3 S21: 0.0488 S22: 0.0113 S23: 0.1569 REMARK 3 S31: -0.1174 S32: -0.2278 S33: -0.0413 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): 14.1670 -0.8860 19.8890 REMARK 3 T TENSOR REMARK 3 T11: -0.1282 T22: -0.0972 REMARK 3 T33: -0.1312 T12: 0.0187 REMARK 3 T13: 0.0214 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 1.4182 L22: 1.3387 REMARK 3 L33: 1.0329 L12: -0.7233 REMARK 3 L13: 0.1418 L23: -0.2239 REMARK 3 S TENSOR REMARK 3 S11: 0.0844 S12: 0.0951 S13: -0.0711 REMARK 3 S21: -0.0873 S22: -0.0698 S23: 0.0146 REMARK 3 S31: 0.0551 S32: 0.0481 S33: -0.0147 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): 8.1510 -4.7930 -1.5470 REMARK 3 T TENSOR REMARK 3 T11: 0.0556 T22: 0.1043 REMARK 3 T33: 0.0324 T12: 0.0692 REMARK 3 T13: -0.0119 T23: -0.0747 REMARK 3 L TENSOR REMARK 3 L11: 14.4211 L22: 5.8233 REMARK 3 L33: 9.9653 L12: 2.3497 REMARK 3 L13: -6.1049 L23: 5.3422 REMARK 3 S TENSOR REMARK 3 S11: -0.0182 S12: 0.3362 S13: -0.0053 REMARK 3 S21: -0.7835 S22: -0.2299 S23: -0.7685 REMARK 3 S31: 0.4105 S32: -0.1729 S33: 0.2481 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.THE SIDE CHAIN OF ARG 75 HAS ALTERNATIVE CONFORMATIONS, REMARK 3 ONE OF WHICH IS ON A DIAD AXIS. IT HAS NOT BEEN MODELLED. REMARK 4 REMARK 4 2CN0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1290028780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-05 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) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91954 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 83900 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.670 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.14 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 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 2CF8.PDB REMARK 200 REMARK 200 REMARK: ISOMORPHOUS TO 2CF8.PDB 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 35.32000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.70500 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 35.70500 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: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.6 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 H2115 LIES ON A SPECIAL POSITION. REMARK 375 HOH H2120 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 THROMBIN,IS RESPONSIBLE FOR BOND CLEAVAGE AFTER ARG AND LYS,AND REMARK 400 SUBSEQUENTLY CONVERTS FIBRINOGEN TO FIBRIN AND ACTIVATES REMARK 400 FACTORS V, VII, VIII, XIII, AND, IN COMPLEX REMARK 400 WITH THROMBOMODULIN, PROTEIN C. REMARK 400 REMARK 400 HIRUDIN ACTS AS A POTENT THROMBIN-SPECIFIC PROTEASE 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: 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 182 CA - CB - SG ANGL. DEV. = 6.7 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 TYR H 60A 82.79 -150.30 REMARK 500 ASN H 60G 80.65 -159.11 REMARK 500 HIS H 71 -59.76 -132.04 REMARK 500 ILE H 79 -62.95 -127.36 REMARK 500 ASN H 95 76.24 -100.78 REMARK 500 GLU H 97A -73.84 -119.07 REMARK 500 PHE L 7 -93.23 -130.53 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 H2022 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH H2030 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH H2033 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH H2336 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH L2059 DISTANCE = 6.37 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 74.3 REMARK 620 3 PHE H 204A O 89.6 89.8 REMARK 620 4 HOH H2233 O 79.9 150.0 75.0 REMARK 620 5 HOH H2246 O 63.0 73.7 150.8 107.7 REMARK 620 6 HOH H2282 O 163.9 90.7 84.5 112.9 118.8 REMARK 620 N 1 2 3 4 5 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 93.4 REMARK 620 3 HOH H2261 O 86.6 94.1 REMARK 620 4 HOH H2262 O 160.6 72.0 81.9 REMARK 620 5 HOH H2302 O 108.7 157.5 83.6 85.6 REMARK 620 6 HOH H2310 O 100.9 82.4 171.8 90.0 96.8 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY A 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 F25 H 1246 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 IIA DBREF 2CN0 H 16 245 UNP P00734 THRB_HUMAN 364 620 DBREF 2CN0 I 1 1 PDB 2CN0 2CN0 1 1 DBREF 2CN0 I 2 11 UNP P28503 ITHC_HIRME 56 65 DBREF 2CN0 L 1 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 11 HET F25 H1246 58 HET NA H1248 1 HET CA H1249 1 HETNAM SIN SUCCINIC ACID HETNAM F25 4-(1R,3AS,4R,8AS,8BR)-[1-DIFLUOROMETHYL-2-(4- HETNAM 2 F25 FLUOROBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN- HETNAM 3 F25 4-YL]BENZAMIDINE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION FORMUL 2 SIN C4 H6 O4 FORMUL 4 F25 C24 H27 F3 N4 O FORMUL 5 NA NA 1+ FORMUL 6 CA CA 2+ FORMUL 7 HOH *397(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 ASP H 170 1 7 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 GLN H 30 ARG H 35 0 SHEET 2 HB 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 3 HB 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 HB 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 HB 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 HB 7 LEU H 64 ILE H 68 -1 O LEU H 64 N LEU H 85 SHEET 7 HB 7 GLN H 30 ARG H 35 -1 O MET H 32 N ARG H 67 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 2.04 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.07 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.02 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.08 LINK C4 SIN I 1 N PHE I 2 1555 1555 1.34 LINK O LYS H 169 CA CA H1249 1555 1555 2.65 LINK O THR H 172 CA CA H1249 1555 1555 2.61 LINK O PHE H 204A CA CA H1249 4546 1555 2.69 LINK O ARG H 221A NA NA H1248 1555 1555 2.28 LINK O LYS H 224 NA NA H1248 1555 1555 2.27 LINK NA NA H1248 O HOH H2261 1555 1555 2.71 LINK NA NA H1248 O HOH H2262 1555 1555 2.49 LINK NA NA H1248 O HOH H2302 1555 1555 2.46 LINK NA NA H1248 O HOH H2310 1555 1555 2.31 LINK CA CA H1249 O HOH H2233 1555 1555 2.77 LINK CA CA H1249 O HOH H2246 1555 1555 2.97 LINK CA CA H1249 O HOH H2282 1555 4546 2.67 CISPEP 1 SER H 36A PRO H 37 0 -4.13 SITE 1 AC1 15 HIS H 57 TYR H 60A GLU H 97A ASN H 98 SITE 2 AC1 15 LEU H 99 ASP H 189 ALA H 190 SER H 214 SITE 3 AC1 15 TRP H 215 GLY H 216 GLY H 219 GLY H 226 SITE 4 AC1 15 HOH H2065 HOH H2313 HOH H2327 SITE 1 AC2 6 ARG H 221A LYS H 224 HOH H2261 HOH H2262 SITE 2 AC2 6 HOH H2302 HOH H2310 SITE 1 AC3 6 LYS H 169 THR H 172 PHE H 204A HOH H2233 SITE 2 AC3 6 HOH H2246 HOH H2282 SITE 1 AC4 15 PHE H 34 GLN H 38 LEU H 65 ARG H 67 SITE 2 AC4 15 ARG H 73 THR H 74 ARG H 75 TYR H 76 SITE 3 AC4 15 ILE H 82 HOH H2111 HOH I2001 HOH I2002 SITE 4 AC4 15 HOH I2003 HOH I2004 HOH I2005 CRYST1 70.640 71.410 72.520 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 0.014004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014017 0.00000