PDB Short entry for 3K65 HEADER HYDROLASE 08-OCT-09 3K65 TITLE CRYSTAL STRUCTURE OF PRETHOMBIN-2/FRAGMENT-2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 199-314; COMPND 5 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 6 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN HEAVY COMPND 7 CHAIN; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PROTHROMBIN; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: RESIDUES 315-622; COMPND 13 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 14 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN HEAVY COMPND 15 CHAIN; COMPND 16 EC: 3.4.21.5; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: PLASMA DERIVED; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: F2; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21STAR(DE3)PLYSS; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PET23PREII(S195A) KEYWDS PROTHROMBIN, COAGULATION, ZYMOGEN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.E.ADAMS,J.A.HUNTINGTON REVDAT 5 06-SEP-23 3K65 1 REMARK REVDAT 4 13-OCT-21 3K65 1 REMARK SEQADV REVDAT 3 05-JUL-17 3K65 1 JRNL REVDAT 2 25-SEP-13 3K65 1 REMARK VERSN REVDAT 1 29-SEP-10 3K65 0 JRNL AUTH T.E.ADAMS,J.A.HUNTINGTON JRNL TITL STRUCTURAL TRANSITIONS DURING PROTHROMBIN ACTIVATION: ON THE JRNL TITL 2 IMPORTANCE OF FRAGMENT 2. JRNL REF BIOCHIMIE V. 122 235 2016 JRNL REFN ISSN 1638-6183 JRNL PMID 26365066 JRNL DOI 10.1016/J.BIOCHI.2015.09.013 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 48634 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) : 0.213 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2443 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2800 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.26800 REMARK 3 B22 (A**2) : 7.26800 REMARK 3 B33 (A**2) : -14.53600 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.450 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.359 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.938 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.940 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 59.31 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : DIOL.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR:CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : DIOL.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3K65 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055594. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48634 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 51.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 369318. REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : 0.09100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37400 REMARK 200 R SYM FOR SHELL (I) : 0.37400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1HAG, 2HPQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% BUFFER 1 MIX, 10% ALCOHOLS MIX, REMARK 280 40% EDO-P8K MIX, PH 6.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 102.94000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.76500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.76500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.47000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.76500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.76500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 154.41000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.76500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.76500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.47000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.76500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.76500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 154.41000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 102.94000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 B 839 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 870 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 SER A 156 REMARK 465 GLU A 157 REMARK 465 GLY A 158 REMARK 465 SER A 159 REMARK 465 SER A 160 REMARK 465 VAL A 161 REMARK 465 ASN A 162 REMARK 465 LEU A 163 REMARK 465 SER A 164 REMARK 465 PRO A 165 REMARK 465 PRO A 166 REMARK 465 LEU A 167 REMARK 465 GLU A 168 REMARK 465 GLU A 249 REMARK 465 GLU A 250 REMARK 465 ALA A 251 REMARK 465 VAL A 252 REMARK 465 GLU A 253 REMARK 465 GLU A 254 REMARK 465 GLU A 255 REMARK 465 THR A 256 REMARK 465 GLY A 257 REMARK 465 ASP A 258 REMARK 465 GLY A 259 REMARK 465 LEU A 260 REMARK 465 ASP A 261 REMARK 465 GLU A 262 REMARK 465 ASP A 263 REMARK 465 SER A 264 REMARK 465 ASP A 265 REMARK 465 ARG A 266 REMARK 465 ALA A 267 REMARK 465 ILE A 268 REMARK 465 GLU A 269 REMARK 465 GLY A 270 REMARK 465 ARG A 271 REMARK 465 THR B 272 REMARK 465 ALA B 273 REMARK 465 THR B 274 REMARK 465 SER B 275 REMARK 465 GLU B 276 REMARK 465 TYR B 277 REMARK 465 GLN B 278 REMARK 465 GLY B 462 REMARK 465 ASN B 463 REMARK 465 LEU B 464 REMARK 465 LYS B 465 REMARK 465 GLU B 466 REMARK 465 THR B 467 REMARK 465 TRP B 468 REMARK 465 THR B 469 REMARK 465 ALA B 470 REMARK 465 ASN B 471 REMARK 465 VAL B 472 REMARK 465 GLY B 473 REMARK 465 LYS B 474 REMARK 465 GLY B 475 REMARK 465 GLU B 514 REMARK 465 GLY B 515 REMARK 465 LYS B 516 REMARK 465 ARG B 517 REMARK 465 GLY B 518 REMARK 465 ASP B 519 REMARK 465 ALA B 520 REMARK 465 CYS B 521 REMARK 465 GLU B 522 REMARK 465 GLU B 549 REMARK 465 GLY B 550 REMARK 465 GLY B 578 REMARK 465 GLU B 579 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 GLN A 169 CG CD OE1 NE2 REMARK 470 LYS A 236 CD CE NZ REMARK 470 LYS B 307 CE NZ REMARK 470 GLU B 314 CG CD OE1 OE2 REMARK 470 ILE B 321 CG1 CG2 CD1 REMARK 470 GLU B 323 CG CD OE1 OE2 REMARK 470 GLN B 344 CG CD OE1 NE2 REMARK 470 LYS B 426 NZ REMARK 470 LYS B 427 NZ REMARK 470 GLU B 444 CG CD OE1 OE2 REMARK 470 GLN B 476 CG CD OE1 NE2 REMARK 470 ARG B 498 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 552 CG OD1 OD2 REMARK 470 ARG B 553 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 554 CG OD1 OD2 REMARK 470 GLN B 576 CD OE1 NE2 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 ASP B 552 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 ARG B 553 N - CA - C ANGL. DEV. = 22.4 DEGREES REMARK 500 ASP B 554 N - CA - C ANGL. DEV. = -19.4 DEGREES REMARK 500 GLY B 555 N - CA - C ANGL. DEV. = -16.6 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 GLU A 216 -123.55 44.66 REMARK 500 ASP A 244 98.34 -66.90 REMARK 500 ASP A 244 99.03 -66.90 REMARK 500 PHE B 299 -83.30 -134.02 REMARK 500 TYR B 367 85.84 -159.59 REMARK 500 ASN B 373 77.97 -154.40 REMARK 500 ILE B 395 -65.04 -134.99 REMARK 500 GLU B 414 -70.30 -121.16 REMARK 500 SER B 432 -169.10 -161.60 REMARK 500 ASP B 524 37.31 -85.31 REMARK 500 SER B 546 -60.97 -108.26 REMARK 500 ARG B 553 37.62 -67.77 REMARK 500 ASP B 554 -70.61 -91.76 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 BU1 A 599 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BU1 A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HAG RELATED DB: PDB REMARK 900 THE ISOMORPHOUS STRUCTURES OF PRETHROMBIN2, HIRUGEN-AND PPACK- REMARK 900 THROMBIN: CHANGES ACCOMPANYING ACTIVATION AND EXOSITE BINDING TO REMARK 900 THROMBIN REMARK 900 RELATED ID: 2HPQ RELATED DB: PDB REMARK 900 STRUCTURES OF THE NONCOVALENT COMPLEXES OF HUMAN AND BOVINE REMARK 900 PROTHROMBIN FRAGMENT 2 WITH HUMAN PPACK-THROMBIN REMARK 900 RELATED ID: 3E6P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MEIZOTHROMBIN DESF1 DBREF 3K65 A 156 271 UNP P00734 THRB_HUMAN 199 314 DBREF 3K65 B 272 579 UNP P00734 THRB_HUMAN 315 622 SEQADV 3K65 ALA B 525 UNP P00734 SER 568 ENGINEERED MUTATION SEQRES 1 A 116 SER GLU GLY SER SER VAL ASN LEU SER PRO PRO LEU GLU SEQRES 2 A 116 GLN CYS VAL PRO ASP ARG GLY GLN GLN TYR GLN GLY ARG SEQRES 3 A 116 LEU ALA VAL THR THR HIS GLY LEU PRO CYS LEU ALA TRP SEQRES 4 A 116 ALA SER ALA GLN ALA LYS ALA LEU SER LYS HIS GLN ASP SEQRES 5 A 116 PHE ASN SER ALA VAL GLN LEU VAL GLU ASN PHE CYS ARG SEQRES 6 A 116 ASN PRO ASP GLY ASP GLU GLU GLY VAL TRP CYS TYR VAL SEQRES 7 A 116 ALA GLY LYS PRO GLY ASP PHE GLY TYR CYS ASP LEU ASN SEQRES 8 A 116 TYR CYS GLU GLU ALA VAL GLU GLU GLU THR GLY ASP GLY SEQRES 9 A 116 LEU ASP GLU ASP SER ASP ARG ALA ILE GLU GLY ARG SEQRES 1 B 308 THR ALA THR SER GLU TYR GLN THR PHE PHE ASN PRO ARG SEQRES 2 B 308 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 3 B 308 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 4 B 308 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG ILE VAL GLU SEQRES 5 B 308 GLY SER ASP ALA GLU ILE GLY MET SER PRO TRP GLN VAL SEQRES 6 B 308 MET LEU PHE ARG LYS SER PRO GLN GLU LEU LEU CYS GLY SEQRES 7 B 308 ALA SER LEU ILE SER ASP ARG TRP VAL LEU THR ALA ALA SEQRES 8 B 308 HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS ASN PHE THR SEQRES 9 B 308 GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS HIS SER ARG SEQRES 10 B 308 THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SER MET LEU SEQRES 11 B 308 GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN TRP ARG GLU SEQRES 12 B 308 ASN LEU ASP ARG ASP ILE ALA LEU MET LYS LEU LYS LYS SEQRES 13 B 308 PRO VAL ALA PHE SER ASP TYR ILE HIS PRO VAL CYS LEU SEQRES 14 B 308 PRO ASP ARG GLU THR ALA ALA SER LEU LEU GLN ALA GLY SEQRES 15 B 308 TYR LYS GLY ARG VAL THR GLY TRP GLY ASN LEU LYS GLU SEQRES 16 B 308 THR TRP THR ALA ASN VAL GLY LYS GLY GLN PRO SER VAL SEQRES 17 B 308 LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU ARG PRO VAL SEQRES 18 B 308 CYS LYS ASP SER THR ARG ILE ARG ILE THR ASP ASN MET SEQRES 19 B 308 PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY LYS ARG GLY SEQRES 20 B 308 ASP ALA CYS GLU GLY ASP ALA GLY GLY PRO PHE VAL MET SEQRES 21 B 308 LYS SER PRO PHE ASN ASN ARG TRP TYR GLN MET GLY ILE SEQRES 22 B 308 VAL SER TRP GLY GLU GLY CYS ASP ARG ASP GLY LYS TYR SEQRES 23 B 308 GLY PHE TYR THR HIS VAL PHE ARG LEU LYS LYS TRP ILE SEQRES 24 B 308 GLN LYS VAL ILE ASP GLN PHE GLY GLU HET BU1 A 599 6 HET BU1 A 600 6 HETNAM BU1 1,4-BUTANEDIOL FORMUL 3 BU1 2(C4 H10 O2) FORMUL 5 HOH *270(H2 O) HELIX 1 1 PRO A 172 GLN A 176 5 5 HELIX 2 2 SER A 196 LYS A 204 1 9 HELIX 3 3 ASN B 282 GLY B 287 1 6 HELIX 4 4 PHE B 299 SER B 303 5 5 HELIX 5 5 THR B 308 LEU B 313 5 6 HELIX 6 6 ALA B 361 CYS B 364 5 4 HELIX 7 7 PRO B 368 ASP B 371 5 4 HELIX 8 8 THR B 375 ASN B 377 5 3 HELIX 9 9 ASP B 442 LEU B 450 1 9 HELIX 10 10 GLU B 489 THR B 497 1 9 HELIX 11 11 LEU B 566 ASP B 575 1 10 SHEET 1 A 2 TRP A 230 TYR A 232 0 SHEET 2 A 2 PHE A 240 TYR A 242 -1 O GLY A 241 N CYS A 231 SHEET 1 B 8 SER B 325 ASP B 326 0 SHEET 2 B 8 GLN B 481 VAL B 488 -1 O VAL B 482 N SER B 325 SHEET 3 B 8 MET B 505 GLY B 509 -1 O CYS B 507 N VAL B 488 SHEET 4 B 8 TYR B 557 HIS B 562 -1 O GLY B 558 N ALA B 508 SHEET 5 B 8 TRP B 539 TRP B 547 -1 N TRP B 547 O PHE B 559 SHEET 6 B 8 PRO B 528 LYS B 532 -1 N MET B 531 O TYR B 540 SHEET 7 B 8 LYS B 455 GLY B 460 -1 N ARG B 457 O VAL B 530 SHEET 8 B 8 GLN B 481 VAL B 488 -1 O LEU B 485 N GLY B 456 SHEET 1 C 7 GLN B 335 ARG B 340 0 SHEET 2 C 7 GLU B 345 LEU B 352 -1 O GLU B 345 N ARG B 340 SHEET 3 C 7 TRP B 357 THR B 360 -1 O LEU B 359 N SER B 351 SHEET 4 C 7 ALA B 421 LEU B 425 -1 O MET B 423 N VAL B 358 SHEET 5 C 7 LYS B 397 ILE B 406 -1 N GLU B 402 O LYS B 424 SHEET 6 C 7 LEU B 379 ILE B 383 -1 N ILE B 383 O LYS B 397 SHEET 7 C 7 GLN B 335 ARG B 340 -1 N PHE B 339 O LEU B 380 SHEET 1 D 2 LEU B 366 TYR B 367 0 SHEET 2 D 2 LYS B 372 ASN B 373 -1 O LYS B 372 N TYR B 367 SSBOND 1 CYS A 170 CYS A 248 1555 1555 2.04 SSBOND 2 CYS A 191 CYS A 231 1555 1555 2.03 SSBOND 3 CYS A 219 CYS A 243 1555 1555 2.02 SSBOND 4 CYS B 293 CYS B 439 1555 1555 2.04 SSBOND 5 CYS B 348 CYS B 364 1555 1555 2.04 SSBOND 6 CYS B 493 CYS B 507 1555 1555 2.04 CISPEP 1 SER B 342 PRO B 343 0 -0.08 SITE 1 AC1 4 ALA A 201 GLY A 235 HOH A 738 HOH A 776 SITE 1 AC2 6 LYS A 236 HOH A 663 HOH A 673 HOH A 706 SITE 2 AC2 6 LEU B 366 ASN B 373 CRYST1 73.530 73.530 205.880 90.00 90.00 90.00 P 41 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 0.013600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013600 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004857 0.00000