HEADER HYDROLASE/HYDROLASE INHIBITOR 18-JUN-07 2V3H TITLE THROMBIN WITH 3-CYCLE NO F 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 IIA; COMPND 9 CHAIN: I; COMPND 10 FRAGMENT: C-TERMINUS, RESIDUES 56-65; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: THE N-TERMINAL ASP IS DES-AMINO - I.E. SUCCINIC ACID; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 15 CHAIN: L; COMPND 16 FRAGMENT: LIGHT CHAIN, RESIDUES 334-361; COMPND 17 EC: 3.4.21.5; COMPND 18 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_COMMON: CHINESE HAMSTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: OVARY; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 12 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 13 ORGANISM_TAXID: 6421; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 19 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: OVARY KEYWDS SERINE PROTEASE INHIBITOR COMPLEX, BLOOD CLOTTING, GAMMA- KEYWDS 2 CARBOXYGLUTAMIC ACID, SERINE PROTEASE, CALCIUM-BINDING, DISEASE KEYWDS 3 MUTATION, BLOOD COAGULATION, SULFATION, ACUTE PHASE, GLYCOPROTEIN, KEYWDS 4 PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.W.BANNER,U.OBST REVDAT 5 07-AUG-13 2V3H 1 REMARK REVDAT 4 13-JUL-11 2V3H 1 VERSN REVDAT 3 24-FEB-09 2V3H 1 VERSN REVDAT 2 01-JUL-08 2V3H 1 SOURCE REVDAT 1 24-JUN-08 2V3H 0 JRNL AUTH K.MUELLER,C.FAEH,F.DIEDERICH JRNL TITL FLUORINE IN PHARMACEUTICALS: LOOKING BEYOND INTUITION. JRNL REF SCIENCE V. 317 1881 2007 JRNL REFN ISSN 0036-8075 JRNL PMID 17901324 JRNL DOI 10.1126/SCIENCE.1131943 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 71.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 29198 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1556 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) : 1947 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2307 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 392 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 27.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : -1.26000 REMARK 3 B33 (A**2) : 0.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.32000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.228 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2424 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3270 ; 1.340 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 6.080 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;30.394 ;23.130 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 429 ;11.868 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;11.621 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 334 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1847 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1083 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1606 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 312 ; 0.152 ; 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): 24 ; 0.159 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.199 ; 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): 1422 ; 0.625 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2293 ; 1.058 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1060 ; 1.771 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 977 ; 2.507 ; 4.500 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): -0.0190 10.7600 24.4330 REMARK 3 T TENSOR REMARK 3 T11: -0.1255 T22: -0.1741 REMARK 3 T33: -0.1446 T12: 0.0366 REMARK 3 T13: 0.0245 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 2.1536 L22: 2.2051 REMARK 3 L33: 2.8037 L12: -0.3417 REMARK 3 L13: -0.2369 L23: -0.9555 REMARK 3 S TENSOR REMARK 3 S11: 0.0478 S12: -0.0362 S13: 0.0685 REMARK 3 S21: 0.0743 S22: -0.0382 S23: 0.0534 REMARK 3 S31: -0.1727 S32: -0.1648 S33: -0.0096 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): 14.2140 -0.9040 19.7180 REMARK 3 T TENSOR REMARK 3 T11: -0.1281 T22: -0.1736 REMARK 3 T33: -0.1405 T12: 0.0193 REMARK 3 T13: 0.0226 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 1.5903 L22: 1.1911 REMARK 3 L33: 1.2537 L12: -0.7605 REMARK 3 L13: 0.0498 L23: -0.1314 REMARK 3 S TENSOR REMARK 3 S11: 0.0775 S12: 0.0870 S13: -0.0487 REMARK 3 S21: -0.0782 S22: -0.0838 S23: -0.0338 REMARK 3 S31: 0.0827 S32: 0.0905 S33: 0.0063 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 2 I 6 REMARK 3 ORIGIN FOR THE GROUP (A): 8.7720 -3.6820 -2.4200 REMARK 3 T TENSOR REMARK 3 T11: 0.1195 T22: 0.1501 REMARK 3 T33: -0.0118 T12: 0.1656 REMARK 3 T13: -0.0105 T23: -0.0536 REMARK 3 L TENSOR REMARK 3 L11: 3.6326 L22: 5.5917 REMARK 3 L33: 15.5361 L12: 4.4784 REMARK 3 L13: -4.7831 L23: -5.0893 REMARK 3 S TENSOR REMARK 3 S11: 0.4861 S12: 0.2002 S13: -0.0217 REMARK 3 S21: -0.6747 S22: -0.8171 S23: -0.6947 REMARK 3 S31: 0.1839 S32: 1.0017 S33: 0.3310 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2V3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-07. REMARK 100 THE PDBE ID CODE IS EBI-32908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MAXFLUX REMARK 200 OPTICS : OSMIC MAXFLUX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 30755 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 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 (%) : 90.4 REMARK 200 DATA REDUNDANCY : 2.740 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.1000 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 (%) : 78.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.71 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.22000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.22000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.89000 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: 3540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.5 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 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 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 HOH H 2106 O HOH H 2245 1.82 REMARK 500 O HOH H 2096 O HOH H 2098 2.09 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 182 CA - CB - SG ANGL. DEV. = 7.3 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 CYS H 42 169.78 179.15 REMARK 500 TYR H 60A 81.83 -153.25 REMARK 500 ASN H 60G 81.83 -154.74 REMARK 500 HIS H 71 -61.90 -124.61 REMARK 500 ILE H 79 -62.30 -129.45 REMARK 500 GLU H 97A -72.75 -118.65 REMARK 500 SER H 214 -77.42 -107.92 REMARK 500 PHE L 7 -94.02 -129.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H1247 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 HOH H2306 O 103.0 REMARK 620 3 LYS H 224 O 99.0 84.9 REMARK 620 4 HOH H2260 O 161.4 89.9 68.5 REMARK 620 5 HOH H2298 O 106.1 94.8 154.3 85.8 REMARK 620 6 HOH H2261 O 88.4 167.5 98.4 80.3 76.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA H1248 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH H2238 O REMARK 620 2 LYS H 169 O 59.2 REMARK 620 3 HOH H2103 O 71.3 117.3 REMARK 620 4 HOH H2239 O 99.7 78.1 74.8 REMARK 620 5 THR H 172 O 74.8 74.3 127.7 150.5 REMARK 620 6 HOH H2281 O 120.7 163.9 75.0 116.5 90.0 REMARK 620 7 PHE H 204A O 151.7 93.3 133.7 79.2 92.1 83.6 REMARK 620 N 1 2 3 4 5 6 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 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 I25 H 1246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA H 1247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 1248 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF HIRUDIN IIA REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2V3O RELATED DB: PDB REMARK 900 THROMBIN WITH 3-CYCLE WITH F DBREF 2V3H H 16 245 UNP P00734 THRB_HUMAN 364 620 DBREF 2V3H I 1 1 PDB 2V3H 2V3H 1 1 DBREF 2V3H I 2 11 UNP P28503 ITHC_HIRME 56 65 DBREF 2V3H 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 I25 H1246 31 HET NA H1247 1 HET CA H1248 1 HETNAM SIN SUCCINIC ACID HETNAM I25 (2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3- HETNAM 2 I25 (DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5- HETNAM 3 I25 ETHYLPHENYL}ACETIC ACID HETNAM NA SODIUM ION HETNAM CA CALCIUM ION FORMUL 2 SIN C4 H6 O4 FORMUL 4 I25 C24 H34 N4 O3 FORMUL 5 NA NA 1+ FORMUL 6 CA CA 2+ FORMUL 7 HOH *392(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 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 2.03 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.02 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.02 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05 LINK NA NA H1247 O ARG H 221A 1555 1555 2.26 LINK NA NA H1247 O HOH H2306 1555 1555 2.25 LINK NA NA H1247 O LYS H 224 1555 1555 2.27 LINK CA CA H1248 O HOH H2238 1555 1555 2.97 LINK CA CA H1248 O LYS H 169 1555 1555 2.59 LINK CA CA H1248 O HOH H2103 1555 1555 3.12 LINK CA CA H1248 O HOH H2239 1555 1555 2.81 LINK CA CA H1248 O THR H 172 1555 1555 2.61 LINK CA CA H1248 O HOH H2281 1555 4546 2.61 LINK CA CA H1248 O PHE H 204A 1555 4546 2.57 LINK C4 SIN I 1 N PHE I 2 1555 1555 1.26 LINK NA NA H1247 O HOH H2260 1555 1555 2.64 LINK NA NA H1247 O HOH H2298 1555 1555 2.66 LINK NA NA H1247 O HOH H2261 1555 1555 2.74 CISPEP 1 SER H 36A PRO H 37 0 -10.63 SITE 1 AC1 16 HIS H 57 TYR H 60A LEU H 99 ASP H 189 SITE 2 AC1 16 ALA H 190 GLU H 192 SER H 195 SER H 214 SITE 3 AC1 16 TRP H 215 GLY H 216 GLY H 219 GLY H 226 SITE 4 AC1 16 HOH H2275 HOH H2296 HOH H2325 HOH H2326 SITE 1 AC2 6 ARG H 221A LYS H 224 HOH H2260 HOH H2261 SITE 2 AC2 6 HOH H2298 HOH H2306 SITE 1 AC3 6 LYS H 169 THR H 172 PHE H 204A HOH H2238 SITE 2 AC3 6 HOH H2239 HOH H2281 SITE 1 AC4 13 PHE H 34 GLN H 38 ARG H 67 ARG H 73 SITE 2 AC4 13 THR H 74 ARG H 75 TYR H 76 ILE H 82 SITE 3 AC4 13 HOH H2117 HOH H2121 HOH H2122 HOH H2124 SITE 4 AC4 13 HOH I2001 CRYST1 70.440 71.780 72.410 90.00 100.40 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 0.014196 0.000000 0.002606 0.00000 SCALE2 0.000000 0.013931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014041 0.00000