10 20 30 40 50 60 70 80 3HKI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 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) : 1.80 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.04 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 28-MAY-09. REMARK 100 THE RCSB ID CODE IS RCSB053245.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 GLU F 59 C - N - CA ANGL. DEV. = 17.1 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 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 GLU F 57 24.5 L L OUTSIDE RANGE REMARK 500 ASP F 58 16.5 L L OUTSIDE RANGE REMARK 500 GLU F 59 19.1 L L OUTSIDE RANGE 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 E1171 DISTANCE = 5.11 ANGSTROMS
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: 3HKJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN THROMBIN MUTANT W215A/E217A IN REMARK 900 COMPLEX 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 SEQADV 3HKI ALA B 217 UNP P19221 GLU 589 ENGINEERED SEQADV 3HKI ALA E 215 UNP P19221 TRP 587 ENGINEERED SEQADV 3HKI ALA E 217 UNP P19221 GLU 589 ENGINEERED
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 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
SITE 1 AC1 1 ASN B 60G SITE 1 AC2 1 ASN E 60G
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