HEADER HYDROLASE 21-OCT-15 5EDK TITLE CRYSTAL STRUCTURE OF PROTHROMBIN DELETION MUTANT RESIDUES 146-167 ( TITLE 2 FORM II ). COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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: MESOCRICETUS AURATUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10036; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: BABY HAMSTER KIDNEY (BHK) KEYWDS PROTHROMBIN, KRINGLE, PROTEASE, COAGULATION FACTOR, ENZYME MECHANISM, KEYWDS 2 KINETICS, STRUCTURE-FUNCTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.POZZI,Z.CHEN,E.DI CERA REVDAT 9 15-NOV-23 5EDK 1 REMARK REVDAT 8 27-SEP-23 5EDK 1 HETSYN REVDAT 7 29-JUL-20 5EDK 1 COMPND REMARK HETNAM LINK REVDAT 7 2 1 SITE ATOM REVDAT 6 04-DEC-19 5EDK 1 REMARK REVDAT 5 06-SEP-17 5EDK 1 REMARK REVDAT 4 09-AUG-17 5EDK 1 JRNL REMARK REVDAT 3 30-MAR-16 5EDK 1 JRNL REVDAT 2 27-JAN-16 5EDK 1 JRNL REVDAT 1 20-JAN-16 5EDK 0 JRNL AUTH N.POZZI,Z.CHEN,E.DI CERA JRNL TITL HOW THE LINKER CONNECTING THE TWO KRINGLES INFLUENCES JRNL TITL 2 ACTIVATION AND CONFORMATIONAL PLASTICITY OF PROTHROMBIN. JRNL REF J.BIOL.CHEM. V. 291 6071 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26763231 JRNL DOI 10.1074/JBC.M115.700401 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.POZZI,Z.CHEN,L.A.PELC,D.B.SHROPSHIRE,E.DI CERA REMARK 1 TITL THE LINKER CONNECTING THE TWO KRINGLES PLAYS A KEY ROLE IN REMARK 1 TITL 2 PROTHROMBIN ACTIVATION. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 111 7630 2014 REMARK 1 REFN ESSN 1091-6490 REMARK 1 PMID 24821807 REMARK 1 DOI 10.1073/PNAS.1403779111 REMARK 2 REMARK 2 RESOLUTION. 3.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 3.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 86.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : -0.900 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 18675 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) : 0.293 REMARK 3 R VALUE (WORKING SET) : 0.291 REMARK 3 FREE R VALUE : 0.323 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1009 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) : 3.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1175 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.4150 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.4510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4241 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.21000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.673 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.520 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.535 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 33.369 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.839 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.779 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4416 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3964 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6003 ; 1.211 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9136 ; 0.784 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 525 ; 8.285 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;35.505 ;23.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 700 ;19.137 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;16.039 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 633 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5012 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1025 ; 0.001 ; 0.020 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): 2109 ; 3.078 ; 8.669 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2108 ; 3.078 ; 8.667 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2631 ; 5.305 ;12.988 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2632 ; 5.304 ;12.990 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2307 ; 2.359 ; 8.761 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2307 ; 2.359 ; 8.761 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3373 ; 4.248 ;13.067 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5071 ; 8.194 ;69.289 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5072 ; 8.193 ;69.289 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5EDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20053 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 86.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44100 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: PHASER REMARK 200 STARTING MODEL: PDB CODE 4O03 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-NA HYDROGEN PHOSPHATE AND 20% REMARK 280 PEG 3350, PH 9.1, VAPOR DIFFUSION, HANGING DROP, 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 173.21350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.09600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.09600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.60675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.09600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.09600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 259.82025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.09600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.09600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.60675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.09600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.09600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 259.82025 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 173.21350 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 1 REMARK 465 ASN A 2 REMARK 465 THR A 3 REMARK 465 PHE A 4 REMARK 465 LEU A 5 REMARK 465 GLU A 233 REMARK 465 THR A 234 REMARK 465 GLY A 235 REMARK 465 ASP A 236 REMARK 465 GLY A 237 REMARK 465 LEU A 238 REMARK 465 ASP A 239 REMARK 465 GLU A 240 REMARK 465 ASP A 241 REMARK 465 SER A 242 REMARK 465 ASP A 243 REMARK 465 ARG A 244 REMARK 465 ALA A 245 REMARK 465 ILE A 246 REMARK 465 GLU A 247 REMARK 465 GLY A 248 REMARK 465 ARG A 249 REMARK 465 THR A 250 REMARK 465 ALA A 251 REMARK 465 ASN A 449 REMARK 465 VAL A 450 REMARK 465 GLY A 451 REMARK 465 LYS A 452 REMARK 465 GLY A 453 REMARK 465 TYR A 558 REMARK 465 LEU A 559 REMARK 465 GLU A 560 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 262 CG CD NE CZ NH1 NH2 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 ARG A 9 -90.44 -72.93 REMARK 500 ASN A 12 103.39 -51.01 REMARK 500 LEU A 13 -53.09 1.86 REMARK 500 CYS A 22 -63.52 -144.34 REMARK 500 TYR A 24 -154.90 73.71 REMARK 500 CGU A 25 -98.13 26.07 REMARK 500 CGU A 26 -41.84 -4.41 REMARK 500 ALA A 27 39.73 -68.72 REMARK 500 PHE A 28 -68.39 -134.74 REMARK 500 ALA A 30 82.27 56.09 REMARK 500 LEU A 31 111.72 -178.71 REMARK 500 SER A 33 71.58 67.44 REMARK 500 GLU A 48 -67.33 -25.82 REMARK 500 ALA A 50 57.37 -103.37 REMARK 500 GLU A 111 -117.76 49.32 REMARK 500 ASN A 116 71.23 -151.13 REMARK 500 GLN A 147 -141.47 75.98 REMARK 500 CYS A 148 82.31 63.12 REMARK 500 GLN A 155 41.23 -105.54 REMARK 500 ARG A 159 18.33 -142.44 REMARK 500 SER A 174 53.22 20.78 REMARK 500 ALA A 175 -66.17 59.29 REMARK 500 SER A 181 -82.26 -62.36 REMARK 500 LYS A 182 5.54 -63.39 REMARK 500 GLN A 184 150.66 116.11 REMARK 500 PHE A 186 -156.32 -122.55 REMARK 500 ALA A 189 35.03 -74.51 REMARK 500 GLU A 194 -105.16 36.85 REMARK 500 ASN A 199 79.33 -109.69 REMARK 500 ASP A 201 41.62 -85.10 REMARK 500 GLU A 227 95.97 -69.79 REMARK 500 GLU A 228 99.72 -65.26 REMARK 500 PRO A 261 -47.95 -27.05 REMARK 500 PHE A 277 -72.41 -125.41 REMARK 500 TYR A 294 86.75 -41.16 REMARK 500 ILE A 295 90.81 -47.53 REMARK 500 ASP A 296 85.10 -35.67 REMARK 500 SER A 310 58.21 -140.51 REMARK 500 SER A 332 -146.11 -163.12 REMARK 500 ARG A 334 -50.34 -157.57 REMARK 500 TRP A 348 -137.52 -97.61 REMARK 500 ASN A 351 89.55 -150.33 REMARK 500 HIS A 364 -50.31 -143.87 REMARK 500 HIS A 385 125.30 -36.16 REMARK 500 ARG A 391 33.93 -78.31 REMARK 500 GLU A 392 -69.20 -167.36 REMARK 500 ASN A 393 25.76 -146.48 REMARK 500 SER A 410 -158.83 -163.44 REMARK 500 ALA A 425 -56.51 89.13 REMARK 500 GLN A 429 -72.12 -99.28 REMARK 500 REMARK 500 THIS ENTRY HAS 62 RAMACHANDRAN OUTLIERS. 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 ASN A 12 LEU A 13 148.14 REMARK 500 TYR A 24 CGU A 25 -143.60 REMARK 500 ASP A 532 GLY A 533 143.49 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 MG A 606 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CGU A 16 OE11 REMARK 620 2 CGU A 26 OE22 73.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 605 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CGU A 19 OE11 REMARK 620 2 CGU A 19 OE21 74.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 608 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CGU A 20 OE22 REMARK 620 2 CGU A 26 OE11 123.0 REMARK 620 3 CGU A 26 OE12 118.7 7.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 607 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CGU A 25 OE22 REMARK 620 2 CGU A 29 OE22 80.6 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4O03 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CA2+ BOUND PROTHROMBIN DELETION MUTANT REMARK 900 RESIDUES 146-167 DBREF 5EDK A 1 557 UNP P00734 THRB_HUMAN 44 622 SEQADV 5EDK MET A 122 UNP P00734 THR 165 VARIANT SEQADV 5EDK A UNP P00734 ASP 189 DELETION SEQADV 5EDK A UNP P00734 GLN 190 DELETION SEQADV 5EDK A UNP P00734 VAL 191 DELETION SEQADV 5EDK A UNP P00734 THR 192 DELETION SEQADV 5EDK A UNP P00734 VAL 193 DELETION SEQADV 5EDK A UNP P00734 ALA 194 DELETION SEQADV 5EDK A UNP P00734 MET 195 DELETION SEQADV 5EDK A UNP P00734 THR 196 DELETION SEQADV 5EDK A UNP P00734 PRO 197 DELETION SEQADV 5EDK A UNP P00734 ARG 198 DELETION SEQADV 5EDK A UNP P00734 SER 199 DELETION SEQADV 5EDK A UNP P00734 GLU 200 DELETION SEQADV 5EDK A UNP P00734 GLY 201 DELETION SEQADV 5EDK A UNP P00734 SER 202 DELETION SEQADV 5EDK A UNP P00734 SER 203 DELETION SEQADV 5EDK A UNP P00734 VAL 204 DELETION SEQADV 5EDK A UNP P00734 ASN 205 DELETION SEQADV 5EDK A UNP P00734 LEU 206 DELETION SEQADV 5EDK A UNP P00734 SER 207 DELETION SEQADV 5EDK A UNP P00734 PRO 208 DELETION SEQADV 5EDK A UNP P00734 PRO 209 DELETION SEQADV 5EDK A UNP P00734 LEU 210 DELETION SEQADV 5EDK TYR A 558 UNP P00734 EXPRESSION TAG SEQADV 5EDK LEU A 559 UNP P00734 EXPRESSION TAG SEQADV 5EDK GLU A 560 UNP P00734 EXPRESSION TAG SEQRES 1 A 560 ALA ASN THR PHE LEU CGU CGU VAL ARG LYS GLY ASN LEU SEQRES 2 A 560 CGU ARG CGU CYS VAL CGU CGU THR CYS SER TYR CGU CGU SEQRES 3 A 560 ALA PHE CGU ALA LEU CGU SER SER THR ALA THR ASP VAL SEQRES 4 A 560 PHE TRP ALA LYS TYR THR ALA CYS GLU THR ALA ARG THR SEQRES 5 A 560 PRO ARG ASP LYS LEU ALA ALA CYS LEU GLU GLY ASN CYS SEQRES 6 A 560 ALA GLU GLY LEU GLY THR ASN TYR ARG GLY HIS VAL ASN SEQRES 7 A 560 ILE THR ARG SER GLY ILE GLU CYS GLN LEU TRP ARG SER SEQRES 8 A 560 ARG TYR PRO HIS LYS PRO GLU ILE ASN SER THR THR HIS SEQRES 9 A 560 PRO GLY ALA ASP LEU GLN GLU ASN PHE CYS ARG ASN PRO SEQRES 10 A 560 ASP SER SER THR MET GLY PRO TRP CYS TYR THR THR ASP SEQRES 11 A 560 PRO THR VAL ARG ARG GLN GLU CYS SER ILE PRO VAL CYS SEQRES 12 A 560 GLY GLN GLU GLN CYS VAL PRO ASP ARG GLY GLN GLN TYR SEQRES 13 A 560 GLN GLY ARG LEU ALA VAL THR THR HIS GLY LEU PRO CYS SEQRES 14 A 560 LEU ALA TRP ALA SER ALA GLN ALA LYS ALA LEU SER LYS SEQRES 15 A 560 HIS GLN ASP PHE ASN SER ALA VAL GLN LEU VAL GLU ASN SEQRES 16 A 560 PHE CYS ARG ASN PRO ASP GLY ASP GLU GLU GLY VAL TRP SEQRES 17 A 560 CYS TYR VAL ALA GLY LYS PRO GLY ASP PHE GLY TYR CYS SEQRES 18 A 560 ASP LEU ASN TYR CYS GLU GLU ALA VAL GLU GLU GLU THR SEQRES 19 A 560 GLY ASP GLY LEU ASP GLU ASP SER ASP ARG ALA ILE GLU SEQRES 20 A 560 GLY ARG THR ALA THR SER GLU TYR GLN THR PHE PHE ASN SEQRES 21 A 560 PRO ARG THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU SEQRES 22 A 560 ARG PRO LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR SEQRES 23 A 560 GLU ARG GLU LEU LEU GLU SER TYR ILE ASP GLY ARG ILE SEQRES 24 A 560 VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO TRP SEQRES 25 A 560 GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU LEU SEQRES 26 A 560 CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU THR SEQRES 27 A 560 ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS ASN SEQRES 28 A 560 PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS HIS SEQRES 29 A 560 SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SER SEQRES 30 A 560 MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN TRP SEQRES 31 A 560 ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS LEU SEQRES 32 A 560 LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO VAL SEQRES 33 A 560 CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU GLN SEQRES 34 A 560 ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN LEU SEQRES 35 A 560 LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN PRO SEQRES 36 A 560 SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU ARG SEQRES 37 A 560 PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR ASP SEQRES 38 A 560 ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY LYS SEQRES 39 A 560 ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO PHE SEQRES 40 A 560 VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN MET SEQRES 41 A 560 GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP GLY SEQRES 42 A 560 LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS LYS SEQRES 43 A 560 TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU TYR LEU SEQRES 44 A 560 GLU MODRES 5EDK CGU A 6 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 7 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 14 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 16 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 19 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 20 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 25 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 26 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 29 GLU MODIFIED RESIDUE MODRES 5EDK CGU A 32 GLU MODIFIED RESIDUE HET CGU A 6 12 HET CGU A 7 12 HET CGU A 14 12 HET CGU A 16 12 HET CGU A 19 12 HET CGU A 20 12 HET CGU A 25 12 HET CGU A 26 12 HET CGU A 29 12 HET CGU A 32 12 HET NAG B 1 14 HET NAG B 2 14 HET NAG A 601 14 HET NAG A 604 14 HET MG A 605 1 HET MG A 606 1 HET MG A 607 1 HET MG A 608 1 HETNAM CGU GAMMA-CARBOXY-GLUTAMIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MG MAGNESIUM 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 FORMUL 1 CGU 10(C6 H9 N O6) FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 5 MG 4(MG 2+) HELIX 1 AA1 ASN A 12 CYS A 17 1 6 HELIX 2 AA2 SER A 33 CYS A 47 1 15 HELIX 3 AA3 PRO A 53 GLU A 62 1 10 HELIX 4 AA4 PRO A 150 GLN A 154 5 5 HELIX 5 AA5 ALA A 175 LEU A 180 1 6 HELIX 6 AA6 ASN A 260 GLY A 265 1 6 HELIX 7 AA7 GLY A 267 CYS A 271 5 5 HELIX 8 AA8 THR A 286 GLU A 292 1 7 HELIX 9 AA9 ALA A 339 CYS A 342 5 4 HELIX 10 AB1 THR A 353 ASN A 355 5 3 HELIX 11 AB2 GLU A 422 ALA A 430 1 9 HELIX 12 AB3 GLU A 467 ASP A 473 1 7 HELIX 13 AB4 LEU A 544 GLY A 556 1 13 SHEET 1 AA1 3 CYS A 86 GLN A 87 0 SHEET 2 AA1 3 TRP A 125 THR A 128 -1 O TYR A 127 N GLN A 87 SHEET 3 AA1 3 ARG A 135 GLU A 137 -1 O GLN A 136 N CYS A 126 SHEET 1 AA2 7 SER A 303 ASP A 304 0 SHEET 2 AA2 7 GLN A 459 VAL A 461 -1 O VAL A 460 N SER A 303 SHEET 3 AA2 7 ARG A 435 GLY A 438 -1 N VAL A 436 O VAL A 461 SHEET 4 AA2 7 PRO A 506 LYS A 510 -1 O VAL A 508 N ARG A 435 SHEET 5 AA2 7 TRP A 517 VAL A 523 -1 O TYR A 518 N MET A 509 SHEET 6 AA2 7 GLY A 536 THR A 539 -1 O THR A 539 N ILE A 522 SHEET 7 AA2 7 MET A 483 ALA A 486 -1 N ALA A 486 O GLY A 536 SHEET 1 AA3 7 GLN A 313 ARG A 318 0 SHEET 2 AA3 7 LEU A 324 LEU A 330 -1 O CYS A 326 N LEU A 316 SHEET 3 AA3 7 TRP A 335 THR A 338 -1 O LEU A 337 N SER A 329 SHEET 4 AA3 7 ALA A 399 LEU A 403 -1 O MET A 401 N VAL A 336 SHEET 5 AA3 7 LYS A 375 ILE A 384 -1 N GLU A 380 O LYS A 402 SHEET 6 AA3 7 LEU A 357 ILE A 361 -1 N VAL A 359 O SER A 377 SHEET 7 AA3 7 GLN A 313 ARG A 318 -1 N MET A 315 O ARG A 360 SHEET 1 AA4 2 LEU A 344 TYR A 345 0 SHEET 2 AA4 2 LYS A 350 ASN A 351 -1 O LYS A 350 N TYR A 345 SSBOND 1 CYS A 17 CYS A 22 1555 1555 2.05 SSBOND 2 CYS A 47 CYS A 60 1555 1555 2.04 SSBOND 3 CYS A 65 CYS A 143 1555 1555 2.03 SSBOND 4 CYS A 86 CYS A 126 1555 1555 2.02 SSBOND 5 CYS A 114 CYS A 138 1555 1555 2.03 SSBOND 6 CYS A 148 CYS A 226 1555 1555 2.04 SSBOND 7 CYS A 169 CYS A 209 1555 1555 2.03 SSBOND 8 CYS A 197 CYS A 221 1555 1555 2.03 SSBOND 9 CYS A 271 CYS A 417 1555 1555 2.03 SSBOND 10 CYS A 326 CYS A 342 1555 1555 2.03 SSBOND 11 CYS A 471 CYS A 485 1555 1555 2.04 SSBOND 12 CYS A 499 CYS A 529 1555 1555 2.03 LINK C CGU A 6 N CGU A 7 1555 1555 1.33 LINK C CGU A 7 N VAL A 8 1555 1555 1.33 LINK C LEU A 13 N CGU A 14 1555 1555 1.33 LINK C CGU A 14 N ARG A 15 1555 1555 1.34 LINK C ARG A 15 N CGU A 16 1555 1555 1.33 LINK C CGU A 16 N CYS A 17 1555 1555 1.33 LINK C VAL A 18 N CGU A 19 1555 1555 1.34 LINK C CGU A 19 N CGU A 20 1555 1555 1.33 LINK C CGU A 20 N THR A 21 1555 1555 1.33 LINK C TYR A 24 N CGU A 25 1555 1555 1.34 LINK C CGU A 25 N CGU A 26 1555 1555 1.34 LINK C CGU A 26 N ALA A 27 1555 1555 1.33 LINK C PHE A 28 N CGU A 29 1555 1555 1.34 LINK C CGU A 29 N ALA A 30 1555 1555 1.33 LINK C LEU A 31 N CGU A 32 1555 1555 1.34 LINK C CGU A 32 N SER A 33 1555 1555 1.34 LINK ND2 ASN A 78 C1 NAG B 1 1555 1555 1.43 LINK ND2 ASN A 100 C1 NAG A 604 1555 1555 1.45 LINK ND2 ASN A 351 C1 NAG A 601 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK OE11 CGU A 16 MG MG A 606 1555 1555 2.48 LINK OE11 CGU A 19 MG MG A 605 1555 1555 2.13 LINK OE21 CGU A 19 MG MG A 605 1555 1555 2.27 LINK OE22 CGU A 20 MG MG A 608 1555 8665 1.93 LINK OE22 CGU A 25 MG MG A 607 1555 1555 2.51 LINK OE22 CGU A 26 MG MG A 606 1555 1555 2.29 LINK OE11 CGU A 26 MG MG A 608 1555 1555 2.63 LINK OE12 CGU A 26 MG MG A 608 1555 1555 2.98 LINK OE22 CGU A 29 MG MG A 607 1555 1555 2.10 CISPEP 1 THR A 52 PRO A 53 0 6.04 CISPEP 2 TYR A 93 PRO A 94 0 -1.19 CISPEP 3 SER A 320 PRO A 321 0 0.62 CRYST1 84.192 84.192 346.427 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 0.011878 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011878 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002887 0.00000 HETATM 1 N CGU A 6 11.499 45.377 90.816 1.00 95.26 N HETATM 2 CA CGU A 6 11.964 46.264 89.715 1.00 92.30 C HETATM 3 C CGU A 6 13.074 45.574 88.976 1.00 95.30 C HETATM 4 O CGU A 6 14.257 45.886 89.132 1.00 91.10 O HETATM 5 CB CGU A 6 12.368 47.624 90.282 1.00 90.75 C HETATM 6 CG CGU A 6 11.423 48.700 89.760 1.00 89.39 C HETATM 7 CD1 CGU A 6 11.794 50.036 90.341 1.00 83.65 C HETATM 8 CD2 CGU A 6 11.445 48.671 88.258 1.00 93.03 C HETATM 9 OE11 CGU A 6 12.275 50.929 89.611 1.00 78.82 O HETATM 10 OE12 CGU A 6 11.589 50.215 91.558 1.00 79.73 O HETATM 11 OE21 CGU A 6 10.352 48.737 87.659 1.00 95.54 O HETATM 12 OE22 CGU A 6 12.541 48.552 87.668 1.00 96.33 O HETATM 13 N CGU A 7 12.670 44.610 88.160 1.00103.91 N HETATM 14 CA CGU A 7 13.587 43.845 87.306 1.00109.19 C HETATM 15 C CGU A 7 13.791 44.629 86.036 1.00110.76 C HETATM 16 O CGU A 7 14.880 44.612 85.455 1.00107.25 O HETATM 17 CB CGU A 7 13.092 42.430 86.962 1.00109.58 C HETATM 18 CG CGU A 7 11.845 41.956 87.718 1.00110.95 C HETATM 19 CD1 CGU A 7 10.602 42.588 87.134 1.00114.06 C HETATM 20 CD2 CGU A 7 11.786 40.455 87.671 1.00108.81 C HETATM 21 OE11 CGU A 7 10.253 42.295 85.970 1.00119.78 O HETATM 22 OE12 CGU A 7 9.960 43.410 87.833 1.00110.78 O HETATM 23 OE21 CGU A 7 11.978 39.884 86.576 1.00105.97 O HETATM 24 OE22 CGU A 7 11.553 39.830 88.731 1.00107.78 O