HEADER HYDROLASE 23-MAY-09 3HKI TITLE CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A IN COMPLEX TITLE 2 WITH THE EXTRACELLULAR FRAGMENT OF HUMAN PAR1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: LIGHT CHAIN: UNP RESIDUES 317-360; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 10 CHAIN: B, E; COMPND 11 FRAGMENT: HEAVY CHAIN: UNP RESIDUES 361-618; COMPND 12 SYNONYM: COAGULATION FACTOR II; COMPND 13 EC: 3.4.21.5; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: PROTEINASE-ACTIVATED RECEPTOR 1; COMPND 18 CHAIN: C, F; COMPND 19 FRAGMENT: EXTRACELLULAR FRAGMENT: UNP RESIDUES 42-62; COMPND 20 SYNONYM: PAR-1, THROMBIN RECEPTOR, COAGULATION FACTOR II RECEPTOR; COMPND 21 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: F2, CF2; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 EXPRESSION_SYSTEM_ORGAN: BABY HAMSTER KIDNEY; SOURCE 9 EXPRESSION_SYSTEM_CELL: BHK CELLS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: HPC4-PNUT; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 GENE: F2, CF2; SOURCE 16 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 18 EXPRESSION_SYSTEM_ORGAN: BABY HAMSTER KIDNEY; SOURCE 19 EXPRESSION_SYSTEM_CELL: BHK CELLS; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: HPC4-PNUT; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: F2R, CF2R, PAR1, TR; SOURCE 26 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 28 EXPRESSION_SYSTEM_ORGAN: BABY HAMSTER KIDNEY; SOURCE 29 EXPRESSION_SYSTEM_CELL: BHK CELLS; SOURCE 30 EXPRESSION_SYSTEM_VECTOR: HPC4-PNUT KEYWDS SERINE PROTEASE, ACUTE PHASE, BLOOD COAGULATION, CLEAVAGE ON PAIR OF KEYWDS 2 BASIC RESIDUES, DISULFIDE BOND, GAMMA-CARBOXYGLUTAMIC ACID, KEYWDS 3 GLYCOPROTEIN, HYDROLASE, KRINGLE, PROTEASE, ZYMOGEN, CELL MEMBRANE, KEYWDS 4 G-PROTEIN COUPLED RECEPTOR, MEMBRANE, PHOSPHOPROTEIN, RECEPTOR, KEYWDS 5 TRANSDUCER, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR P.S.GANDHI,M.J.PAGE,Z.CHEN,L.BUSH-PELC,E.DI CERA REVDAT 6 06-SEP-23 3HKI 1 REMARK REVDAT 5 13-OCT-21 3HKI 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3HKI 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 13-JUL-11 3HKI 1 VERSN REVDAT 2 15-SEP-09 3HKI 1 JRNL REVDAT 1 07-JUL-09 3HKI 0 JRNL AUTH P.S.GANDHI,M.J.PAGE,Z.CHEN,L.BUSH-PELC,E.DI CERA JRNL TITL MECHANISM OF THE ANTICOAGULANT ACTIVITY OF THROMBIN MUTANT JRNL TITL 2 W215A/E217A. JRNL REF J.BIOL.CHEM. V. 284 24098 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19586901 JRNL DOI 10.1074/JBC.M109.025403 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.O.PINEDA,Z.W.CHEN,S.CACCIA,A.M.CANTWELL,S.N.SAVVIDES, REMARK 1 AUTH 2 G.WAKSMAN,F.S.MATHEWS,E.DI CERA REMARK 1 TITL THE ANTICOAGULANT THROMBIN MUTANT W215A/E217A HAS A REMARK 1 TITL 2 COLLAPSED PRIMARY SPECIFICITY POCKET. REMARK 1 REF J.BIOL.CHEM. V. 279 39824 2004 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15252033 REMARK 1 DOI 10.1074/JBC.M407272200 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 150926.620 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 44003 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 SET) : 0.228 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT : 3592 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5769 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 500 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5009 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.040 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.650 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.490 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053245. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : BENT GE(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45052 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1TQ0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL PH 8.5, 20% PEG 10000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 115.70950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.49750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 115.70950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.49750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY CONSISTS OF A, B AND C CHAINS. 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: 3110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 REMARK 350 BIOMOLECULE: 2 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: 3210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 ILE A 14K REMARK 465 ASP A 14L REMARK 465 GLY A 14M REMARK 465 ARG A 15 REMARK 465 THR B 149A REMARK 465 ASN B 149B REMARK 465 ILE B 149C REMARK 465 SER C 42 REMARK 465 PHE C 43 REMARK 465 LEU C 44 REMARK 465 LEU C 45 REMARK 465 LYS C 61 REMARK 465 ASN C 62 REMARK 465 ARG D 15 REMARK 465 THR E 149A REMARK 465 ASN E 149B REMARK 465 ILE E 149C REMARK 465 ASP E 221 REMARK 465 ARG E 221A REMARK 465 LYS E 222 REMARK 465 SER F 42 REMARK 465 PHE F 43 REMARK 465 LEU F 44 REMARK 465 LEU F 45 REMARK 465 ARG F 46 REMARK 465 ASN F 47 REMARK 465 PRO F 48 REMARK 465 ASN F 49 REMARK 465 ASP F 50 REMARK 465 GLU F 60 REMARK 465 LYS F 61 REMARK 465 ASN F 62 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 GLU E 146 CB CG CD OE1 OE2 REMARK 470 TRP E 148 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP E 148 CZ3 CH2 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 LEU B 65 CA - CB - CG ANGL. DEV. = 15.9 DEGREES REMARK 500 GLY B 223 N - CA - C ANGL. DEV. = -15.3 DEGREES REMARK 500 ASP F 58 N - CA - C ANGL. DEV. = 30.1 DEGREES REMARK 500 GLU F 59 C - N - CA ANGL. DEV. = 17.1 DEGREES REMARK 500 GLU F 59 N - CA - C ANGL. DEV. = 17.5 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 THR A 1N -179.47 -42.18 REMARK 500 PHE A 1M -18.94 -156.56 REMARK 500 PHE A 7 -76.83 -128.07 REMARK 500 GLU A 8 -70.50 -56.34 REMARK 500 LYS A 9 -19.24 -42.26 REMARK 500 THR A 14A -12.99 -46.52 REMARK 500 THR A 14B 11.42 -144.37 REMARK 500 GLU B 18 54.67 71.05 REMARK 500 SER B 36A 119.76 -173.68 REMARK 500 TYR B 60A 83.15 -159.31 REMARK 500 ASN B 60G 76.27 -156.71 REMARK 500 HIS B 71 -63.57 -128.07 REMARK 500 ASN B 78 -8.95 72.04 REMARK 500 SER B 115 -166.53 -163.85 REMARK 500 VAL B 129 -76.17 -60.56 REMARK 500 THR B 129A -12.53 -48.59 REMARK 500 TRP B 148 35.13 74.53 REMARK 500 GLU B 149E 129.55 115.62 REMARK 500 PRO B 166 -37.44 -38.59 REMARK 500 ARG B 187 -117.84 -97.47 REMARK 500 PHE B 204A -85.75 -76.19 REMARK 500 ALA B 215 80.12 -157.29 REMARK 500 CYS B 220 -135.73 56.29 REMARK 500 LYS B 222 109.85 25.91 REMARK 500 LYS B 224 -75.43 -61.23 REMARK 500 ILE B 242 -73.43 -59.88 REMARK 500 ASN C 47 -70.51 1.50 REMARK 500 GLU C 57 168.83 -48.69 REMARK 500 PHE D 7 -83.12 -130.89 REMARK 500 GLU E 39 144.47 175.85 REMARK 500 TYR E 60A 85.43 -155.60 REMARK 500 ASN E 60G 81.26 -156.58 REMARK 500 HIS E 71 -62.05 -137.71 REMARK 500 VAL E 79 -54.53 -133.61 REMARK 500 SER E 115 -162.56 -169.95 REMARK 500 GLU E 146 36.40 -79.75 REMARK 500 THR E 147 169.76 138.42 REMARK 500 TRP E 148 -169.78 -122.41 REMARK 500 GLU E 149E -7.05 -42.36 REMARK 500 VAL E 186 -53.70 -27.74 REMARK 500 ARG E 187 -105.77 -83.34 REMARK 500 ASN E 205 12.08 58.83 REMARK 500 PHE F 55 -21.45 -145.80 REMARK 500 ASP F 58 -146.63 88.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TQ0 RELATED DB: PDB REMARK 900 THE ANTICOAGULANT THROMBIN MUTANT W215A/E217A HAS A COLLAPSED REMARK 900 PRIMARY SPECIFICITY POCKET REMARK 900 RELATED ID: 3HK3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A (ONE REMARK 900 MOLECULE IN THE ASYMMETRIC UNIT) REMARK 900 RELATED ID: 3HK6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A (TWO REMARK 900 MOLECULES IN THE ASYMMETRIC UNIT) REMARK 900 RELATED ID: 3HKJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THROMBIN MUTANT W215A/E217A IN COMPLEX REMARK 900 WITH THE EXTRACELLULAR FRAGMENT OF HUMAN PAR1 DBREF 3HKI A 1P 15 UNP P19221 THRB_MOUSE 317 360 DBREF 3HKI B 16 246 UNP P19221 THRB_MOUSE 361 618 DBREF 3HKI C 42 62 UNP P25116 PAR1_HUMAN 42 62 DBREF 3HKI D 1P 15 UNP P19221 THRB_MOUSE 317 360 DBREF 3HKI E 16 246 UNP P19221 THRB_MOUSE 361 618 DBREF 3HKI F 42 62 UNP P25116 PAR1_HUMAN 42 62 SEQADV 3HKI ALA B 215 UNP P19221 TRP 587 ENGINEERED MUTATION SEQADV 3HKI ALA B 217 UNP P19221 GLU 589 ENGINEERED MUTATION SEQADV 3HKI ALA E 215 UNP P19221 TRP 587 ENGINEERED MUTATION SEQADV 3HKI ALA E 217 UNP P19221 GLU 589 ENGINEERED MUTATION SEQRES 1 A 44 PHE HIS THR PHE PHE ASN GLU LYS THR PHE GLY LEU GLY SEQRES 2 A 44 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 3 A 44 SER LEU LYS ASP THR THR GLU LYS GLU LEU LEU ASP SER SEQRES 4 A 44 TYR ILE ASP GLY ARG SEQRES 1 B 258 ILE VAL GLU GLY TRP ASP ALA GLU LYS GLY ILE ALA PRO SEQRES 2 B 258 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 258 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 258 THR ALA ALA HIS CYS ILE LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 258 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 258 HIS SER ARG THR ARG TYR GLU ARG ASN VAL GLU LYS ILE SEQRES 7 B 258 SER MET LEU GLU LYS ILE TYR VAL HIS PRO ARG TYR ASN SEQRES 8 B 258 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS SEQRES 9 B 258 LEU LYS LYS PRO VAL PRO PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 258 VAL CYS LEU PRO ASP LYS GLN THR VAL THR SER LEU LEU SEQRES 11 B 258 ARG ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 258 LEU ARG GLU THR TRP THR THR ASN ILE ASN GLU ILE GLN SEQRES 13 B 258 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 258 ARG PRO VAL CYS LYS ALA SER THR ARG ILE ARG ILE THR SEQRES 15 B 258 ASP ASN MET PHE CYS ALA GLY PHE LYS VAL ASN ASP THR SEQRES 16 B 258 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 258 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 258 MET GLY ILE VAL SER ALA GLY ALA GLY CYS ASP ARG LYS SEQRES 19 B 258 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 258 ARG TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY SEQRES 1 C 21 SER PHE LEU LEU ARG ASN PRO ASN ASP LYS TYR GLU PRO SEQRES 2 C 21 PHE TRP GLU ASP GLU GLU LYS ASN SEQRES 1 D 44 PHE HIS THR PHE PHE ASN GLU LYS THR PHE GLY LEU GLY SEQRES 2 D 44 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 3 D 44 SER LEU LYS ASP THR THR GLU LYS GLU LEU LEU ASP SER SEQRES 4 D 44 TYR ILE ASP GLY ARG SEQRES 1 E 258 ILE VAL GLU GLY TRP ASP ALA GLU LYS GLY ILE ALA PRO SEQRES 2 E 258 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 E 258 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 E 258 THR ALA ALA HIS CYS ILE LEU TYR PRO PRO TRP ASP LYS SEQRES 5 E 258 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 E 258 HIS SER ARG THR ARG TYR GLU ARG ASN VAL GLU LYS ILE SEQRES 7 E 258 SER MET LEU GLU LYS ILE TYR VAL HIS PRO ARG TYR ASN SEQRES 8 E 258 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS SEQRES 9 E 258 LEU LYS LYS PRO VAL PRO PHE SER ASP TYR ILE HIS PRO SEQRES 10 E 258 VAL CYS LEU PRO ASP LYS GLN THR VAL THR SER LEU LEU SEQRES 11 E 258 ARG ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 E 258 LEU ARG GLU THR TRP THR THR ASN ILE ASN GLU ILE GLN SEQRES 13 E 258 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 E 258 ARG PRO VAL CYS LYS ALA SER THR ARG ILE ARG ILE THR SEQRES 15 E 258 ASP ASN MET PHE CYS ALA GLY PHE LYS VAL ASN ASP THR SEQRES 16 E 258 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 E 258 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 E 258 MET GLY ILE VAL SER ALA GLY ALA GLY CYS ASP ARG LYS SEQRES 19 E 258 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 E 258 ARG TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY SEQRES 1 F 21 SER PHE LEU LEU ARG ASN PRO ASN ASP LYS TYR GLU PRO SEQRES 2 F 21 PHE TRP GLU ASP GLU GLU LYS ASN MODRES 3HKI ASN B 60G ASN GLYCOSYLATION SITE MODRES 3HKI ASN E 60G ASN GLYCOSYLATION SITE HET NAG B 301 14 HET NAG E 301 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 7 NAG 2(C8 H15 N O6) FORMUL 9 HOH *217(H2 O) HELIX 1 1 ASN A 1K GLY A 1F 1 6 HELIX 2 2 GLY A 1D CYS A 1 5 5 HELIX 3 3 PHE A 7 SER A 11 5 5 HELIX 4 4 THR A 14B TYR A 14J 1 9 HELIX 5 5 ALA B 55 CYS B 58 5 4 HELIX 6 6 PRO B 60B ASP B 60E 5 4 HELIX 7 7 ASP B 125 LEU B 130 1 9 HELIX 8 8 GLU B 164 ALA B 170 1 7 HELIX 9 9 CYS B 191 SER B 195 5 5 HELIX 10 10 GLY B 219 LYS B 222 5 5 HELIX 11 11 LEU B 234 GLY B 246 1 13 HELIX 12 12 ARG C 46 ASP C 50 5 5 HELIX 13 13 ASN D 1K GLY D 1F 1 6 HELIX 14 14 GLY D 1D CYS D 1 5 5 HELIX 15 15 THR D 14B ASP D 14L 1 11 HELIX 16 16 ALA E 55 ILE E 59 1 5 HELIX 17 17 PRO E 60B ASP E 60E 5 4 HELIX 18 18 THR E 60I ASN E 62 5 3 HELIX 19 19 ASP E 125 LEU E 130 1 9 HELIX 20 20 GLU E 164 SER E 171 1 8 HELIX 21 21 CYS E 191 SER E 195 5 5 HELIX 22 22 VAL E 231 GLY E 246 1 16 SHEET 1 A 7 TRP B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N TRP B 20 SHEET 3 A 7 LYS B 135 GLY B 140 -1 N GLY B 136 O LEU B 160 SHEET 4 A 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 A 7 TRP B 207 ALA B 215 -1 O TYR B 208 N MET B 201 SHEET 6 A 7 GLY B 226 HIS B 230 -1 O PHE B 227 N ALA B 215 SHEET 7 A 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 B 7 GLN B 30 ARG B 35 0 SHEET 2 B 7 GLU B 39 LEU B 46 -1 O GLU B 39 N ARG B 35 SHEET 3 B 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 4 B 7 ALA B 104 LEU B 108 -1 O LEU B 106 N VAL B 52 SHEET 5 B 7 LYS B 81 VAL B 90 -1 N TYR B 89 O LEU B 105 SHEET 6 B 7 LEU B 64 ILE B 68 -1 N ILE B 68 O LYS B 81 SHEET 7 B 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 SHEET 1 C 2 LEU B 60 TYR B 60A 0 SHEET 2 C 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A SHEET 1 D 8 TRP E 20 ASP E 21 0 SHEET 2 D 8 GLN E 156 VAL E 163 -1 O VAL E 157 N TRP E 20 SHEET 3 D 8 MET E 180 ALA E 183 -1 O CYS E 182 N VAL E 163 SHEET 4 D 8 GLY E 226 HIS E 230 -1 O TYR E 228 N PHE E 181 SHEET 5 D 8 TRP E 207 ALA E 215 -1 N ALA E 215 O PHE E 227 SHEET 6 D 8 PRO E 198 LYS E 202 -1 N MET E 201 O TYR E 208 SHEET 7 D 8 LYS E 135 GLY E 140 -1 N ARG E 137 O VAL E 200 SHEET 8 D 8 GLN E 156 VAL E 163 -1 O LEU E 160 N GLY E 136 SHEET 1 E 7 LYS E 81 SER E 83 0 SHEET 2 E 7 LEU E 64 ILE E 68 -1 N ILE E 68 O LYS E 81 SHEET 3 E 7 GLN E 30 ARG E 35 -1 N PHE E 34 O LEU E 65 SHEET 4 E 7 GLU E 39 LEU E 46 -1 O LEU E 41 N LEU E 33 SHEET 5 E 7 TRP E 51 THR E 54 -1 O LEU E 53 N SER E 45 SHEET 6 E 7 ALA E 104 LEU E 108 -1 O LEU E 106 N VAL E 52 SHEET 7 E 7 LEU E 85 VAL E 90 -1 N LYS E 87 O LYS E 107 SHEET 1 F 2 LEU E 60 TYR E 60A 0 SHEET 2 F 2 LYS E 60F ASN E 60G-1 O LYS E 60F N TYR E 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.03 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.04 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.05 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.04 SSBOND 5 CYS D 1 CYS E 122 1555 1555 2.03 SSBOND 6 CYS E 42 CYS E 58 1555 1555 2.04 SSBOND 7 CYS E 168 CYS E 182 1555 1555 2.04 SSBOND 8 CYS E 191 CYS E 220 1555 1555 2.05 LINK ND2 ASN B 60G C1 NAG B 301 1555 1555 1.46 LINK ND2 ASN E 60G C1 NAG E 301 1555 1555 1.46 CISPEP 1 SER B 36A PRO B 37 0 0.03 CISPEP 2 SER E 36A PRO E 37 0 0.17 CRYST1 231.419 50.995 80.540 90.00 90.00 90.00 P 21 21 2 8 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 0.004321 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012416 0.00000