HEADER BLOOD CLOTTING,HYDROLASE 26-JUL-05 2AFQ TITLE 1.9 ANGSTROM CRYSTAL STRUCTURE OF WILD-TYPE HUMAN THROMBIN IN THE TITLE 2 SODIUM FREE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: LIGHT CHAIN; 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: PROTHROMBIN; COMPND 10 CHAIN: B, D; COMPND 11 FRAGMENT: HEAVY CHAIN; COMPND 12 SYNONYM: COAGULATION FACTOR II; COMPND 13 EC: 3.4.21.5; COMPND 14 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23(+)-PRE2; 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: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET23(+)-PRE2 KEYWDS ALPHA-THROMBIN; COAGULATION; ALLOSTERY; PROTEASE; COAGULATION FACTOR KEYWDS 2 II, BLOOD CLOTTING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.J.D.JOHNSON,T.E.ADAMS,J.A.HUNTINGTON REVDAT 7 23-AUG-23 2AFQ 1 REMARK REVDAT 6 14-DEC-16 2AFQ 1 TITLE REVDAT 5 16-NOV-11 2AFQ 1 HETATM REVDAT 4 13-JUL-11 2AFQ 1 VERSN REVDAT 3 24-FEB-09 2AFQ 1 VERSN REVDAT 2 22-NOV-05 2AFQ 1 DBREF REVDAT 1 15-NOV-05 2AFQ 0 JRNL AUTH D.J.D.JOHNSON,T.E.ADAMS,W.LI,J.A.HUNTINGTON JRNL TITL CRYSTAL STRUCTURE OF WILD-TYPE HUMAN THROMBIN IN THE JRNL TITL 2 NA+-FREE STATE JRNL REF BIOCHEM.J. V. 392 21 2005 JRNL REFN ISSN 0264-6021 JRNL PMID 16201969 JRNL DOI 10.1042/BJ20051217 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2052606.875 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49279 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) : 0.197 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1513 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7805 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 250 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4326 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 478 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.70000 REMARK 3 B22 (A**2) : -2.62000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 1.370 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.240 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.020 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.030 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 58.59 REMARK 3 REMARK 3 NCS MODEL : RESTRAINTS 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 : PROTEIN.TOP REMARK 3 PARAMETER FILE 2 : WATER_REP.TOP REMARK 3 PARAMETER FILE 3 : GOL.TOP REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_REP.PARAM REMARK 3 TOPOLOGY FILE 2 : WATER_REP.PARAM REMARK 3 TOPOLOGY FILE 3 : GOL.PAR REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8700 REMARK 200 MONOCHROMATOR : TRIANGULAR SINGLE CRYSTAL SI REMARK 200 OPTICS : RH COATED SI MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49378 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 50.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : 0.10300 REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : 0.55000 REMARK 200 FOR SHELL : 1.100 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 1PPB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MAGNESIUM ACETATE, LITHIUM REMARK 280 CHLORIDE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 76.67000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.15500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 76.67000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.15500 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH D 663 LIES ON A SPECIAL POSITION. 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 LEU B 143A REMARK 465 LYS B 143B REMARK 465 GLU B 143C REMARK 465 THR B 143D REMARK 465 TRP B 143E REMARK 465 THR B 143F REMARK 465 ALA B 143G REMARK 465 ASN B 143H REMARK 465 VAL B 143I REMARK 465 GLY B 143J REMARK 465 LYS B 143K REMARK 465 GLY B 143L REMARK 465 GLN B 143M REMARK 465 PRO B 143N REMARK 465 ASN D 142A REMARK 465 LEU D 142B REMARK 465 LYS D 142C REMARK 465 GLU D 142D REMARK 465 THR D 142E REMARK 465 TRP D 142F REMARK 465 THR D 142G REMARK 465 ALA D 142H REMARK 465 ASN D 142I REMARK 465 VAL D 142J REMARK 465 GLY D 142K REMARK 465 LYS D 142L REMARK 465 GLY D 142M REMARK 465 GLN D 142N REMARK 465 ASP D 186A REMARK 465 GLU D 186B REMARK 465 GLY D 186C REMARK 465 LYS D 186D REMARK 465 PHE D 245 REMARK 465 GLY D 246 REMARK 465 GLU D 247 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 A 1C CD OE1 OE2 REMARK 470 ARG A 14D NE CZ NH1 NH2 REMARK 470 ARG B 75 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 77 CG CD OE1 OE2 REMARK 470 ARG B 77A CD NE CZ NH1 NH2 REMARK 470 ASN B 78 CG OD1 ND2 REMARK 470 ARG B 97 CZ NH1 NH2 REMARK 470 LYS B 236 CD CE NZ REMARK 470 GLU B 247 CD OE1 OE2 REMARK 470 THR D 74 CG2 REMARK 470 TYR D 76 OH REMARK 470 ARG D 77A CG CD NE CZ NH1 NH2 REMARK 470 GLU D 127 CG CD OE1 OE2 REMARK 470 GLU D 164 CD OE1 OE2 REMARK 470 ARG D 173 CZ NH1 NH2 REMARK 470 ARG D 187 NE CZ NH1 NH2 REMARK 470 LYS D 236 CG CD CE NZ 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 PHE A 7 -89.14 -129.52 REMARK 500 TYR B 60A 83.46 -157.89 REMARK 500 ASN B 78 -8.59 72.94 REMARK 500 ASN B 98 12.29 -141.95 REMARK 500 GLU B 186B 51.12 -117.91 REMARK 500 CYS B 220 -104.99 62.60 REMARK 500 CYS B 220 -104.66 64.72 REMARK 500 PHE C 7 -88.97 -130.45 REMARK 500 TYR D 60A 85.09 -164.28 REMARK 500 ASN D 60G 70.82 -150.89 REMARK 500 ARG D 77A -75.72 -17.27 REMARK 500 ASN D 78 37.03 -98.94 REMARK 500 ILE D 79 -56.26 -135.54 REMARK 500 ASN D 98 12.85 -142.60 REMARK 500 CYS D 220 -96.55 60.26 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 GOL D 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 1007 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PPB RELATED DB: PDB REMARK 900 HUMAN ALPHA-THROMBIN BOUND TO PPACK REMARK 900 RELATED ID: 1HAH RELATED DB: PDB REMARK 900 WILD-TYPE THROMBIN BOUND TO HIRUGEN REMARK 900 RELATED ID: 1RD3 RELATED DB: PDB REMARK 900 E217K THROMBIN DBREF 2AFQ A 1D 14K UNP P00734 THRB_HUMAN 332 360 DBREF 2AFQ C 1D 14K UNP P00734 THRB_HUMAN 332 360 DBREF 2AFQ B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 2AFQ D 16 247 UNP P00734 THRB_HUMAN 364 622 SEQRES 1 A 29 GLY GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS SEQRES 2 A 29 LYS SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SEQRES 3 A 29 SER TYR ILE 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 TRP GLY GLU 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 29 GLY GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS SEQRES 2 C 29 LYS SER LEU GLU ASP LYS THR GLU ARG GLU LEU LEU GLU SEQRES 3 C 29 SER TYR ILE SEQRES 1 D 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 D 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 D 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 D 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 D 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 D 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 D 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 D 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 D 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 D 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 D 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 D 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 D 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 D 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 D 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 D 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 D 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 D 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 D 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 D 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU HET GOL B1002 12 HET GOL B1004 6 HET GOL B1005 6 HET GOL D1001 12 HET GOL D1003 6 HET GOL D1006 6 HET GOL D1007 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 7(C3 H8 O3) FORMUL 12 HOH *478(H2 O) HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 THR A 14B SER A 14I 1 8 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 SER B 171 1 8 HELIX 8 8 CYS B 191 SER B 195 5 5 HELIX 9 9 LEU B 234 GLY B 246 1 13 HELIX 10 10 PHE C 7 SER C 11 5 5 HELIX 11 11 THR C 14B ILE C 14K 1 10 HELIX 12 12 ALA D 55 CYS D 58 5 4 HELIX 13 13 PRO D 60B ASP D 60E 5 4 HELIX 14 14 THR D 60I ASN D 62 5 3 HELIX 15 15 ASP D 125 LEU D 130 1 9 HELIX 16 16 GLU D 164 SER D 171 1 8 HELIX 17 17 CYS D 191 SER D 195 5 5 HELIX 18 18 LEU D 234 GLN D 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 GLY B 140 O GLN B 156 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 GLY B 216 -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 TRP 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 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 ALA B 104 N THR B 54 SHEET 5 B 7 LYS B 81 ILE B 90 -1 N GLU B 86 O LYS B 107 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 D 20 ASP D 21 0 SHEET 2 D 7 GLN D 156 PRO D 161 -1 O VAL D 157 N SER D 20 SHEET 3 D 7 LYS D 135 GLY D 140 -1 N GLY D 140 O GLN D 156 SHEET 4 D 7 PRO D 198 LYS D 202 -1 O VAL D 200 N ARG D 137 SHEET 5 D 7 TRP D 207 GLY D 216 -1 O TYR D 208 N MET D 201 SHEET 6 D 7 GLY D 226 HIS D 230 -1 O PHE D 227 N TRP D 215 SHEET 7 D 7 MET D 180 ALA D 183 -1 N PHE D 181 O TYR D 228 SHEET 1 E 7 LYS D 81 SER D 83 0 SHEET 2 E 7 LEU D 64 ILE D 68 -1 N ILE D 68 O LYS D 81 SHEET 3 E 7 GLN D 30 ARG D 35 -1 N PHE D 34 O LEU D 65 SHEET 4 E 7 GLU D 39 LEU D 46 -1 O LEU D 41 N LEU D 33 SHEET 5 E 7 TRP D 51 THR D 54 -1 O LEU D 53 N SER D 45 SHEET 6 E 7 ALA D 104 LEU D 108 -1 O MET D 106 N VAL D 52 SHEET 7 E 7 LEU D 85 ILE D 90 -1 N GLU D 86 O LYS D 107 SHEET 1 F 2 LEU D 60 TYR D 60A 0 SHEET 2 F 2 LYS D 60F ASN D 60G-1 O LYS D 60F N TYR D 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.04 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.03 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.04 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.03 SSBOND 5 CYS C 1 CYS D 122 1555 1555 2.04 SSBOND 6 CYS D 42 CYS D 58 1555 1555 2.03 SSBOND 7 CYS D 168 CYS D 182 1555 1555 2.04 SSBOND 8 CYS D 191 CYS D 220 1555 1555 2.04 CISPEP 1 SER B 36A PRO B 37 0 -0.19 CISPEP 2 SER D 36A PRO D 37 0 -0.38 SITE 1 AC1 9 HIS D 57 TYR D 60A LEU D 99 HOH D 302 SITE 2 AC1 9 HOH D 413 HOH D 602 HOH D 634 HOH D 637 SITE 3 AC1 9 HOH D 761 SITE 1 AC2 8 HIS B 57 TYR B 60A GLU B 192 TRP B 215 SITE 2 AC2 8 HOH B 336 HOH B 552 HOH B 612 HOH B 640 SITE 1 AC3 3 PRO D 111 PRO D 166 ASP D 170 SITE 1 AC4 5 ALA B 129A HIS B 230 PHE B 232 ARG B 233 SITE 2 AC4 5 HOH B 648 SITE 1 AC5 6 PHE B 34 GLN B 38 ARG B 67 ARG B 73 SITE 2 AC5 6 HOH B 464 HOH B 642 SITE 1 AC6 1 ASP D 116 SITE 1 AC7 10 ASP B 222 HOH B 369 LEU D 41 CYS D 42 SITE 2 AC7 10 HIS D 57 LYS D 60F GLU D 192 GLY D 193 SITE 3 AC7 10 SER D 195 HOH D 522 CRYST1 153.340 82.310 50.930 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 0.006521 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019635 0.00000