HEADER HYDROLASE 15-AUG-08 3E6P TITLE CRYSTAL STRUCTURE OF HUMAN MEIZOTHROMBIN DESF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: ACTIVATION PEPTIDE FRAGMENT 2 AND THROMBIN LIGHT CHAIN: UNP COMPND 5 RESIDUES 206-363; COMPND 6 SYNONYM: COAGULATION FACTOR II [CONTAINS: ACTIVATION PEPTIDE FRAGMENT COMPND 7 1; ACTIVATION PEPTIDE FRAGMENT 2; THROMBIN LIGHT CHAIN; THROMBIN COMPND 8 HEAVY CHAIN]; COMPND 9 EC: 3.4.21.5; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: PROTHROMBIN; COMPND 13 CHAIN: H; COMPND 14 FRAGMENT: THROMBIN HEAVY CHAIN: UNP RESIDUES 364-622; COMPND 15 SYNONYM: COAGULATION FACTOR II [CONTAINS: ACTIVATION PEPTIDE FRAGMENT COMPND 16 1; ACTIVATION PEPTIDE FRAGMENT 2; THROMBIN LIGHT CHAIN; THROMBIN COMPND 17 HEAVY CHAIN]; COMPND 18 EC: 3.4.21.5; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: F2; SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 EXPRESSION_SYSTEM_CELL: BABY HAMSTER KIDNEY CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: HPC4-PNUT; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: F2; SOURCE 15 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 16 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 18 EXPRESSION_SYSTEM_CELL: BABY HAMSTER KIDNEY CELLS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: HPC4-PNUT KEYWDS THROMBIN, MEIZOTHROMBIN, ALLOSTERY, LINKAGE, NA+ BINDING, ACUTE KEYWDS 2 PHASE, BLOOD COAGULATION, CLEAVAGE ON PAIR OF BASIC RESIDUES, KEYWDS 3 DISEASE MUTATION, GAMMA-CARBOXYGLUTAMIC ACID, GLYCOPROTEIN, KEYWDS 4 HYDROLASE, KRINGLE, PROTEASE, SECRETED, SERINE PROTEASE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR M.E.PAPACONSTANTINOU,P.GANDHI,Z.CHEN,A.BAH,E.DI CERA REVDAT 7 30-AUG-23 3E6P 1 REMARK HETSYN REVDAT 6 29-JUL-20 3E6P 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 13-JUL-11 3E6P 1 VERSN REVDAT 4 09-JUN-09 3E6P 1 REVDAT REVDAT 3 24-FEB-09 3E6P 1 VERSN REVDAT 2 02-DEC-08 3E6P 1 JRNL REVDAT 1 18-NOV-08 3E6P 0 JRNL AUTH M.E.PAPACONSTANTINOU,P.S.GANDHI,Z.CHEN,A.BAH,E.DI CERA JRNL TITL NA(+) BINDING TO MEIZOTHROMBIN DESF1. JRNL REF CELL.MOL.LIFE SCI. V. 65 3688 2008 JRNL REFN ISSN 1420-682X JRNL PMID 18854941 JRNL DOI 10.1007/S00018-008-8502-7 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.D.MARTIN,M.G.MALKOWSKI,J.BOX,C.T.ESMON,B.F.EDWARDS REMARK 1 TITL NEW INSIGHTS INTO THE REGULATION OF THE BLOOD CLOTTING REMARK 1 TITL 2 CASCADE DERIVED FROM THE X-RAY CRYSTAL STRUCTURE OF BOVINE REMARK 1 TITL 3 MEIZOTHROMBIN DES F1 IN COMPLEX WITH PPACK. REMARK 1 REF STRUCTURE V. 5 1681 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 9438869 REMARK 1 DOI 10.1016/S0969-2126(97)00314-6 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 38428 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 + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2026 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2192 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3203 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.50 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3360 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4546 ; 1.741 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 398 ; 6.988 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;36.918 ;23.952 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 557 ;19.530 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;19.575 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 471 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2591 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1994 ; 1.021 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3200 ; 1.938 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1366 ; 2.741 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1346 ; 4.284 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. RESIDUES L251-L286 WERE MODELED USING REMARK 3 BOVINE MEIZOTHROMBIN (PDB ID CODE 1A0H) AND ASSIGNED AN REMARK 3 OCCUPANCY OF ZERO DUE TO LACK OF ELECTRON DENSITY. 3. RESIDUES REMARK 3 WITH MISSING ATOMS LISTED IN REMARK 470 ARE DUE TO LACK OF REMARK 3 ELECTRON DENSITY FOR SIDE CHAINS AND WERE MODELED AS ALANINES. REMARK 4 REMARK 4 3E6P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 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 : SI(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 : 40469 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 ENTRIES 1A0H, 1SHH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA2(SO4), 23% PEG 3350, PH 6.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 50.10200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 60.66800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.66800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.05100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.66800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.66800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.15300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.66800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.66800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.05100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.66800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.66800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.15300 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 50.10200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, A 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 LEU L 163 REMARK 465 SER L 164 REMARK 465 PRO L 165 REMARK 465 PRO L 166 REMARK 465 LEU L 167 REMARK 465 GLU L 168 REMARK 465 GLY L 414M REMARK 465 ARG L 415 REMARK 465 THR H 149 REMARK 465 ALA H 149A REMARK 465 ASN H 149B REMARK 465 VAL H 149C REMARK 465 GLY H 149D REMARK 465 LYS H 149E REMARK 465 GLY H 246 REMARK 465 GLU H 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 TRP H 148 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP H 148 CZ3 CH2 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA L 251 REMARK 475 VAL L 252 REMARK 475 GLU L 253 REMARK 475 GLU L 254 REMARK 475 GLU L 255 REMARK 475 THR L 256 REMARK 475 GLY L 257 REMARK 475 ASP L 258 REMARK 475 GLY L 259 REMARK 475 LEU L 260 REMARK 475 ASP L 261 REMARK 475 GLU L 262 REMARK 475 ASP L 263 REMARK 475 SER L 264 REMARK 475 ASP L 265 REMARK 475 ARG L 266 REMARK 475 ALA L 267 REMARK 475 ILE L 268 REMARK 475 GLU L 269 REMARK 475 GLY L 270 REMARK 475 ARG L 271 REMARK 475 THR L 272 REMARK 475 ALA L 273 REMARK 475 THR L 274 REMARK 475 SER L 275 REMARK 475 GLU L 276 REMARK 475 TYR L 277 REMARK 475 GLN L 278 REMARK 475 THR L 279 REMARK 475 PHE L 280 REMARK 475 PHE L 281 REMARK 475 ASN L 282 REMARK 475 PRO L 283 REMARK 475 ARG L 284 REMARK 475 THR L 285 REMARK 475 PHE L 286 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG L 174 O GLY L 224 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU H 217 C GLY H 219 N 0.246 REMARK 500 REMARK 500 REMARK: NULL 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 PHE L 286 CB - CA - C ANGL. DEV. = -21.8 DEGREES REMARK 500 PHE L 286 CA - C - O ANGL. DEV. = -27.9 DEGREES REMARK 500 PHE L 286 CA - C - N ANGL. DEV. = 20.1 DEGREES REMARK 500 LEU H 65 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 ARG H 67 NE - CZ - NH1 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG H 75 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 GLU H 217 O - C - N ANGL. DEV. = -25.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR L 178 129.39 -175.74 REMARK 500 ALA L 211 6.60 -59.09 REMARK 500 GLU L 216 -113.98 66.19 REMARK 500 ASN L 221 70.87 -116.01 REMARK 500 ALA L 234 -167.67 -163.66 REMARK 500 THR L 256 -17.58 -41.26 REMARK 500 ASP L 258 -57.44 -121.58 REMARK 500 LEU L 260 -110.92 -80.79 REMARK 500 ASP L 261 119.67 78.46 REMARK 500 SER L 264 25.30 87.93 REMARK 500 ASP L 265 -161.78 -122.40 REMARK 500 ARG L 266 -60.64 -136.22 REMARK 500 ILE L 268 84.49 22.16 REMARK 500 GLU L 269 -75.65 -71.19 REMARK 500 THR L 272 68.13 -159.24 REMARK 500 GLN L 278 79.43 75.54 REMARK 500 PHE L 280 -79.52 -109.13 REMARK 500 ARG L 284 -92.48 -138.82 REMARK 500 THR L 285 74.69 -118.68 REMARK 500 PHE L 407 -81.19 -131.48 REMARK 500 GLU H 39 129.52 -170.16 REMARK 500 ARG H 50 8.45 -151.37 REMARK 500 TYR H 60A 83.61 -150.11 REMARK 500 ASN H 60G 82.37 -160.86 REMARK 500 HIS H 71 -58.49 -146.07 REMARK 500 GLU H 77 57.89 -97.72 REMARK 500 ASN H 78 -8.50 89.58 REMARK 500 GLU H 97A -74.24 -111.11 REMARK 500 ASN H 98 15.33 -142.32 REMARK 500 SER H 115 -167.50 -160.25 REMARK 500 ASP H 186A 8.23 84.37 REMARK 500 SER H 214 -62.66 -120.41 REMARK 500 ARG H 233 -9.60 -58.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE L 286 GLY L 401F -48.86 REMARK 500 GLU H 217 GLY H 219 -149.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE L 286 -16.05 REMARK 500 GLU H 217 27.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 90.5 REMARK 620 3 HOH H1003 O 160.7 75.0 REMARK 620 4 HOH H1005 O 100.2 167.7 95.8 REMARK 620 5 HOH H1006 O 92.0 100.7 78.6 85.1 REMARK 620 6 HOH H1007 O 87.7 75.2 100.4 99.0 175.9 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A0H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE MEIZOTHROMBIN DES F1 IN COMPLEX WITH REMARK 900 PPACK DBREF 3E6P L 163 415 UNP P00734 THRB_HUMAN 206 363 DBREF 3E6P H 16 247 UNP P00734 THRB_HUMAN 364 622 SEQRES 1 L 158 LEU SER PRO PRO LEU GLU GLN CYS VAL PRO ASP ARG GLY SEQRES 2 L 158 GLN GLN TYR GLN GLY ARG LEU ALA VAL THR THR HIS GLY SEQRES 3 L 158 LEU PRO CYS LEU ALA TRP ALA SER ALA GLN ALA LYS ALA SEQRES 4 L 158 LEU SER LYS HIS GLN ASP PHE ASN SER ALA VAL GLN LEU SEQRES 5 L 158 VAL GLU ASN PHE CYS ARG ASN PRO ASP GLY ASP GLU GLU SEQRES 6 L 158 GLY VAL TRP CYS TYR VAL ALA GLY LYS PRO GLY ASP PHE SEQRES 7 L 158 GLY TYR CYS ASP LEU ASN TYR CYS GLU GLU ALA VAL GLU SEQRES 8 L 158 GLU GLU THR GLY ASP GLY LEU ASP GLU ASP SER ASP ARG SEQRES 9 L 158 ALA ILE GLU GLY ARG THR ALA THR SER GLU TYR GLN THR SEQRES 10 L 158 PHE PHE ASN PRO ARG THR PHE GLY SER GLY GLU ALA ASP SEQRES 11 L 158 CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SER LEU GLU SEQRES 12 L 158 ASP LYS THR GLU ARG GLU LEU LEU GLU SER TYR ILE ASP SEQRES 13 L 158 GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU MODRES 3E6P ASN H 60G ASN GLYCOSYLATION SITE HET NAG A 1 14 HET NAG A 2 14 HET SO4 L 303 5 HET DFK H 301 30 HET NA H 302 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETNAM DFK D-PHENYLALANYL-N-[(1S)-4-{[(Z)-AMINO(IMINO) HETNAM 2 DFK METHYL]AMINO}-1-(CHLOROACETYL)BUTYL]-L-PROLINAMIDE HETNAM NA SODIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN DFK D-PHENYLALANYL-PROLYL-ARGINYL-CHLOROMETHANE FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 4 SO4 O4 S 2- FORMUL 5 DFK C21 H34 N6 O3 FORMUL 6 NA NA 1+ FORMUL 7 HOH *208(H2 O) HELIX 1 1 PRO L 172 GLN L 176 5 5 HELIX 2 2 SER L 196 LYS L 204 1 9 HELIX 3 3 GLY L 401D CYS L 401 5 5 HELIX 4 4 PHE L 407 SER L 411 5 5 HELIX 5 5 THR L 414B ASP L 414L 1 11 HELIX 6 6 ALA H 55 CYS H 58 5 4 HELIX 7 7 PRO H 60B ASP H 60E 5 4 HELIX 8 8 THR H 60I ASN H 62 5 3 HELIX 9 9 ASP H 125 LEU H 130 1 9 HELIX 10 10 GLU H 164 SER H 171 1 8 HELIX 11 11 LEU H 234 GLN H 244 1 11 SHEET 1 A 2 TRP L 230 TYR L 232 0 SHEET 2 A 2 PHE L 240 TYR L 242 -1 O GLY L 241 N CYS L 231 SHEET 1 B 7 SER H 20 ASP H 21 0 SHEET 2 B 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 B 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 B 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 B 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 B 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 B 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 C 7 LYS H 81 SER H 83 0 SHEET 2 C 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 3 C 7 GLN H 30 ARG H 35 -1 N MET H 32 O ARG H 67 SHEET 4 C 7 GLU H 39 LEU H 46 -1 O LEU H 41 N LEU H 33 SHEET 5 C 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 6 C 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 7 C 7 LEU H 85 ILE H 90 -1 N LYS H 87 O LYS H 107 SHEET 1 D 2 LEU H 60 TYR H 60A 0 SHEET 2 D 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS L 170 CYS L 248 1555 1555 2.08 SSBOND 2 CYS L 191 CYS L 231 1555 1555 2.08 SSBOND 3 CYS L 219 CYS L 243 1555 1555 2.06 SSBOND 4 CYS L 401 CYS H 122 1555 1555 2.11 SSBOND 5 CYS H 42 CYS H 58 1555 1555 2.05 SSBOND 6 CYS H 168 CYS H 182 1555 1555 2.08 SSBOND 7 CYS H 191 CYS H 220 1555 1555 2.12 LINK NE2 HIS H 57 CH2 DFK H 301 1555 1555 1.33 LINK ND2 ASN H 60G C1 NAG A 1 1555 1555 1.45 LINK OG SER H 195 C3 DFK H 301 1555 1555 1.37 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.46 LINK O ARG H 221A NA NA H 302 1555 1555 2.45 LINK O LYS H 224 NA NA H 302 1555 1555 2.26 LINK NA NA H 302 O HOH H1003 1555 1555 2.23 LINK NA NA H 302 O HOH H1005 1555 1555 2.20 LINK NA NA H 302 O HOH H1006 1555 1555 2.53 LINK NA NA H 302 O HOH H1007 1555 1555 2.49 CISPEP 1 SER H 36A PRO H 37 0 -8.92 CRYST1 121.336 121.336 100.204 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 0.008242 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008242 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009980 0.00000