10 20 30 40 50 60 70 80 3HKJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 23-MAY-09 3HKJ
TITLE CRYSTAL STRUCTURE OF HUMAN THROMBIN MUTANT W215A/E217A IN COMPLEX WITH TITLE 2 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 333-363; 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 364-622; 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: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F2; 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: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: F2; 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, DISEASE MUTATION, DISULFIDE BOND, GAMMA- KEYWDS 3 CARBOXYGLUTAMIC ACID, GLYCOPROTEIN, HYDROLASE, KRINGLE, PROTEASE, KEYWDS 4 SECRETED, ZYMOGEN, CELL MEMBRANE, G-PROTEIN COUPLED RECEPTOR, KEYWDS 5 MEMBRANE, PHOSPHOPROTEIN, RECEPTOR, TRANSDUCER, TRANSMEMBRANE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.S.GANDHI,M.J.PAGE,Z.CHEN,L.BUSH-PELC,E.DI CERA
REVDAT 3 13-JUL-11 3HKJ 1 VERSN REVDAT 2 15-SEP-09 3HKJ 1 JRNL REVDAT 1 07-JUL-09 3HKJ 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 127702.590 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 22129 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) : 0.196 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1079 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2898 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 157 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4682 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.80 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.32 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) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.83 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 3HKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-09. REMARK 100 THE RCSB ID CODE IS RCSB053246.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : 22864 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 93.4 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 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 (%): 56.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.5, 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 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.5 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: 2090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.8 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 ALA B 149A REMARK 465 ASN B 149B REMARK 465 VAL B 149C REMARK 465 GLY B 149D REMARK 465 LYS B 149E REMARK 465 ASP B 222 REMARK 465 GLY B 223 REMARK 465 SER C 42 REMARK 465 PHE C 43 REMARK 465 LEU C 44 REMARK 465 LEU C 45 REMARK 465 ARG C 46 REMARK 465 ASN C 47 REMARK 465 PRO C 48 REMARK 465 ASP C 58 REMARK 465 GLU C 59 REMARK 465 GLU C 60 REMARK 465 LYS C 61 REMARK 465 ASN C 62 REMARK 465 GLU D 1C REMARK 465 GLY D 14M REMARK 465 ARG D 15 REMARK 465 THR E 149 REMARK 465 ALA E 149A REMARK 465 ASN E 149B REMARK 465 VAL E 149C REMARK 465 GLY E 149D REMARK 465 LYS E 149E REMARK 465 GLU E 186B REMARK 465 GLY E 186C REMARK 465 ASP E 222 REMARK 465 GLU E 247 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 58 REMARK 465 GLU F 59 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 ARG B 221A CG CD NE CZ NH1 NH2 REMARK 470 ARG E 221A 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 GLY E 188 N - CA - C ANGL. DEV. = 19.2 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 ALA A 1B -54.88 71.16 REMARK 500 PHE A 7 -84.94 -135.21 REMARK 500 ASP A 14L 111.82 112.86 REMARK 500 ALA B 44 -179.71 -173.24 REMARK 500 ASP B 49 -5.79 -54.87 REMARK 500 TYR B 60A 85.98 -163.03 REMARK 500 ASP B 60E 57.41 36.41 REMARK 500 ASN B 60G 62.94 -151.73 REMARK 500 HIS B 71 -67.17 -134.55 REMARK 500 ILE B 79 -67.38 -141.98 REMARK 500 GLU B 97A -74.90 -95.06 REMARK 500 ASN B 98 27.83 -147.99 REMARK 500 THR B 147 105.36 -54.41 REMARK 500 GLU B 186B -19.86 -43.47 REMARK 500 ARG B 187 -163.70 -73.02 REMARK 500 ALA B 215 88.15 -160.17 REMARK 500 ALA B 217 10.70 -64.88 REMARK 500 CYS B 220 48.24 -70.74 REMARK 500 ASP C 50 89.29 -176.40 REMARK 500 TRP C 56 166.01 100.91 REMARK 500 PHE D 7 -78.96 -138.74 REMARK 500 SER D 11 28.85 49.50 REMARK 500 SER E 36A 118.76 -162.44 REMARK 500 LEU E 41 -69.62 -94.94 REMARK 500 ALA E 44 -177.20 -172.90 REMARK 500 ARG E 50 -5.87 -142.24 REMARK 500 TYR E 60A 86.25 -162.88 REMARK 500 ASN E 60G 79.62 -157.14 REMARK 500 HIS E 71 -55.08 -132.29 REMARK 500 ILE E 79 -57.33 -122.84 REMARK 500 GLU E 97A -20.73 -154.75 REMARK 500 ASN E 98 13.82 -160.09 REMARK 500 SER E 115 -169.26 -162.67 REMARK 500 ARG E 187 93.94 177.35 REMARK 500 ASP E 189 -158.15 -160.66 REMARK 500 ASN E 204B 10.56 -151.87 REMARK 500 ALA E 215 98.52 -165.35 REMARK 500 CYS E 220 -6.26 70.63 REMARK 500 PHE E 245 -2.86 59.23 REMARK 500 TRP F 56 -60.69 83.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP E 221 24.5 L L OUTSIDE RANGE REMARK 500 PHE F 55 23.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG E 301
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TQ0 RELATED DB: PDB REMARK 900 THE ANTICOAGULANT THROMBIN MUTANT W215A/E217A HAS A REMARK 900 COLLAPSED PRIMARY SPECIFICITY POCKET REMARK 900 RELATED ID: 3HK3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A REMARK 900 (ONE MOLECULE IN THE ASYMMETRIC UNIT) REMARK 900 RELATED ID: 3HK6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A REMARK 900 (TWO MOLECULES IN THE ASYMMETRIC UNIT) REMARK 900 RELATED ID: 3HKI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE THROMBIN MUTANT W215A/E217A IN REMARK 900 COMPLEX WITH THE EXTRACELLULAR FRAGMENT OF HUMAN PAR1
DBREF 3HKJ A 1C 15 UNP P00734 THRB_HUMAN 333 363 DBREF 3HKJ B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3HKJ C 42 62 UNP P25116 PAR1_HUMAN 42 62 DBREF 3HKJ D 1C 15 UNP P00734 THRB_HUMAN 333 363 DBREF 3HKJ E 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3HKJ F 42 62 UNP P25116 PAR1_HUMAN 42 62
SEQADV 3HKJ ALA B 215 UNP P00734 TRP 590 ENGINEERED SEQADV 3HKJ ALA B 217 UNP P00734 GLU 592 ENGINEERED SEQADV 3HKJ ALA E 215 UNP P00734 TRP 590 ENGINEERED SEQADV 3HKJ ALA E 217 UNP P00734 GLU 592 ENGINEERED
SEQRES 1 A 31 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 A 31 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER SEQRES 3 A 31 TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER ALA GLY ALA GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 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 31 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 D 31 SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SER SEQRES 3 D 31 TYR ILE ASP GLY ARG SEQRES 1 E 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 E 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 E 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 E 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 E 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 E 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 E 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 E 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 E 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 E 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 E 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 E 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 E 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 E 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 E 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 E 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 E 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 E 259 MET GLY ILE VAL SER ALA GLY ALA GLY CYS ASP ARG ASP SEQRES 19 E 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 E 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU 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 3HKJ ASN B 60G ASN GLYCOSYLATION SITE MODRES 3HKJ ASN E 60G ASN GLYCOSYLATION SITE
HET NAG B 301 14 HET NAG E 301 14
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
FORMUL 7 NAG 2(C8 H15 N O6) FORMUL 9 HOH *154(H2 O)
HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 THR A 14B ASP A 14L 1 11 HELIX 3 3 ALA B 55 CYS B 58 5 4 HELIX 4 4 PRO B 60B ASP B 60E 5 4 HELIX 5 5 THR B 60I ASN B 62 5 3 HELIX 6 6 ASP B 125 LEU B 130 1 9 HELIX 7 7 GLU B 164 ASP B 170 1 7 HELIX 8 8 CYS B 191 SER B 195 5 5 HELIX 9 9 LEU B 234 PHE B 245 1 12 HELIX 10 10 PHE D 7 SER D 11 5 5 HELIX 11 11 THR D 14B ASP D 14L 1 11 HELIX 12 12 ALA E 55 CYS E 58 5 4 HELIX 13 13 PRO E 60B ASP E 60E 5 4 HELIX 14 14 ASP E 125 LEU E 130 1 9 HELIX 15 15 GLU E 164 SER E 171 1 8 HELIX 16 16 CYS E 191 SER E 195 5 5 HELIX 17 17 LEU E 234 GLN E 244 1 11
SHEET 1 A 7 SER B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 A 7 LYS B 135 GLY B 140 -1 N VAL B 138 O VAL B 158 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 THR B 229 N ILE B 212 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 SER B 48 -1 O LEU B 41 N LEU B 33 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 MET B 106 N VAL B 52 SHEET 5 B 7 LYS B 81 ILE 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 7 SER E 20 ASP E 21 0 SHEET 2 D 7 GLN E 156 PRO E 161 -1 O VAL E 157 N SER E 20 SHEET 3 D 7 LYS E 135 GLY E 140 -1 N GLY E 136 O LEU E 160 SHEET 4 D 7 PRO E 198 LYS E 202 -1 O VAL E 200 N ARG E 137 SHEET 5 D 7 TRP E 207 ALA E 215 -1 O TYR E 208 N MET E 201 SHEET 6 D 7 GLY E 226 HIS E 230 -1 O PHE E 227 N ALA E 215 SHEET 7 D 7 MET E 180 ALA E 183 -1 N PHE E 181 O TYR E 228 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 MET E 106 N VAL E 52 SHEET 7 E 7 LEU E 85 ILE E 90 -1 N TYR E 89 O LEU E 105 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 2.05 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.04 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.02 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.04 SSBOND 5 CYS D 1 CYS E 122 1555 1555 2.04 SSBOND 6 CYS E 42 CYS E 58 1555 1555 2.04 SSBOND 7 CYS E 168 CYS E 182 1555 1555 2.03 SSBOND 8 CYS E 191 CYS E 220 1555 1555 2.04
LINK ND2 ASN B 60G C1 NAG B 301 1555 1555 1.47 LINK ND2 ASN E 60G C1 NAG E 301 1555 1555 1.47
CISPEP 1 SER B 36A PRO B 37 0 -0.02 CISPEP 2 SER E 36A PRO E 37 0 -0.18
SITE 1 AC1 3 ASN B 60G HOH B1122 HOH B1132 SITE 1 AC2 1 ASN E 60G
CRYST1 53.140 61.783 67.834 98.78 110.28 92.95 P 1 2
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 0.018818 0.000971 0.007251 0.00000
SCALE2 0.000000 0.016207 0.003000 0.00000
SCALE3 0.000000 0.000000 0.015983 0.00000