HEADER HYDROLASE 13-DEC-13 4O03 TITLE CRYSTAL STRUCTURE OF CA2+ BOUND PROTHROMBIN DELETION MUTANT RESIDUES TITLE 2 146-167 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.5; COMPND 5 ENGINEERED: YES; COMPND 6 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: CRICETINAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10026; SOURCE 8 EXPRESSION_SYSTEM_CELL: BABY HAMSTER KIDNEY (BHK) KEYWDS PROTHROMBIN, KRINGLE, SERINE PROTEASE, COAGULATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.POZZI,Z.CHEN,D.B.SHROPSHIRE,L.A.PELC,E.DI CERA REVDAT 6 06-DEC-23 4O03 1 REMARK REVDAT 5 20-SEP-23 4O03 1 HETSYN REVDAT 4 29-JUL-20 4O03 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 23-AUG-17 4O03 1 SOURCE REMARK REVDAT 2 25-JUN-14 4O03 1 JRNL REVDAT 1 21-MAY-14 4O03 0 JRNL AUTH N.POZZI,Z.CHEN,L.A.PELC,D.B.SHROPSHIRE,E.DI CERA JRNL TITL THE LINKER CONNECTING THE TWO KRINGLES PLAYS A KEY ROLE IN JRNL TITL 2 PROTHROMBIN ACTIVATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 7630 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24821807 JRNL DOI 10.1073/PNAS.1403779111 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.HUANG,A.C.RIGBY,X.MORELLI,M.A.GRANT,G.HUANG,B.FURIE REMARK 1 TITL STRUCTURAL BASIS OF MEMBRANE BINDING BY GLA DOMAINS OF REMARK 1 TITL 2 VITAMIN K-DEPENDENT PROTEINS. REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 10 751 2003 REMARK 1 REFN ISSN 1545-9993 REMARK 2 REMARK 2 RESOLUTION. 3.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 3.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : -0.700 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 15753 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) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 835 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) : 3.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 985 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4321 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 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) : 73.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -0.17000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.515 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.430 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.650 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.874 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.813 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4483 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6093 ; 1.650 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 537 ; 8.397 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;40.199 ;24.181 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 733 ;23.777 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;20.261 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 630 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3505 ; 0.008 ; 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): 2679 ; 0.639 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4312 ; 1.196 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1804 ; 1.148 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1781 ; 2.040 ; 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 : 1.40 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 4O03 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083872. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : MIRROR 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 : 16635 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.380 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 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 FROM CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 4NZQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7.5, 10% PEG 4000 AND REMARK 280 5% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 88.72950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.71550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 88.72950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.71550 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A 272 REMARK 465 ALA A 273 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 54 CG CD NE CZ NH1 NH2 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 LEU A 5 C CGU A 6 N 0.161 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 LEU A 5 O - C - N ANGL. DEV. = 10.0 DEGREES REMARK 500 CYS A 65 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 CYS A 170 CA - CB - SG ANGL. DEV. = 8.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 3 77.42 -55.42 REMARK 500 PHE A 4 -108.59 58.51 REMARK 500 LEU A 5 -86.79 -56.62 REMARK 500 CGU A 6 7.09 7.56 REMARK 500 SER A 33 150.75 137.48 REMARK 500 SER A 34 34.82 -98.35 REMARK 500 THR A 35 81.64 -62.02 REMARK 500 ASP A 38 -85.92 150.42 REMARK 500 TYR A 44 -72.46 -78.19 REMARK 500 THR A 49 5.17 -56.47 REMARK 500 ARG A 51 -0.91 -165.25 REMARK 500 THR A 52 -152.47 -79.72 REMARK 500 PRO A 53 -170.59 -68.29 REMARK 500 ARG A 54 -37.44 -39.03 REMARK 500 THR A 71 22.26 -77.29 REMARK 500 ARG A 74 48.14 -141.72 REMARK 500 SER A 101 46.05 -88.85 REMARK 500 THR A 102 -41.34 -144.85 REMARK 500 GLU A 111 -128.45 59.74 REMARK 500 SER A 119 88.64 57.83 REMARK 500 PRO A 131 -7.53 -55.86 REMARK 500 CYS A 170 92.82 79.22 REMARK 500 ARG A 174 21.53 45.82 REMARK 500 HIS A 187 7.65 -62.99 REMARK 500 ALA A 195 -57.72 -11.11 REMARK 500 SER A 196 164.95 -49.82 REMARK 500 LYS A 200 -66.69 -93.62 REMARK 500 GLU A 216 -104.44 48.06 REMARK 500 ASN A 217 42.48 -140.26 REMARK 500 ASP A 223 31.54 -72.50 REMARK 500 TRP A 230 -167.73 -162.42 REMARK 500 CYS A 231 153.77 179.27 REMARK 500 LYS A 236 149.60 -38.54 REMARK 500 ASP A 239 163.63 -44.75 REMARK 500 PHE A 240 176.24 178.75 REMARK 500 GLU A 290 -70.59 -67.14 REMARK 500 ALA A 291 -3.14 -49.43 REMARK 500 ASP A 292 59.12 -142.24 REMARK 500 PHE A 299 -80.21 -143.07 REMARK 500 SER A 303 47.18 38.57 REMARK 500 GLU A 311 -16.34 -47.58 REMARK 500 ASP A 318 79.42 -63.77 REMARK 500 ILE A 321 78.91 105.95 REMARK 500 LYS A 341 -71.45 -68.31 REMARK 500 GLU A 345 137.28 -173.73 REMARK 500 SER A 354 -172.62 -175.51 REMARK 500 THR A 360 -157.96 -148.89 REMARK 500 HIS A 386 -51.08 -126.86 REMARK 500 ARG A 390 151.88 -41.54 REMARK 500 ILE A 395 -71.04 -122.02 REMARK 500 REMARK 500 THIS ENTRY HAS 72 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 ALA A 36 THR A 37 -144.37 REMARK 500 THR A 52 PRO A 53 -146.19 REMARK 500 LEU A 69 GLY A 70 -145.95 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 CA A 604 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 1 O REMARK 620 2 CGU A 6 OE11 122.5 REMARK 620 3 CGU A 7 OE22 134.4 58.6 REMARK 620 4 CGU A 16 OE21 61.6 99.1 156.6 REMARK 620 5 CGU A 16 OE22 92.2 56.0 113.3 43.5 REMARK 620 6 CGU A 26 OE11 108.9 128.6 86.4 105.1 126.1 REMARK 620 7 CGU A 26 OE22 66.6 151.2 137.9 59.3 98.8 52.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 605 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CGU A 6 OE12 REMARK 620 2 CGU A 16 OE22 71.0 REMARK 620 3 CGU A 16 OE21 108.0 50.5 REMARK 620 4 CGU A 20 OE12 127.2 92.4 96.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CGU A 7 OE12 REMARK 620 2 CGU A 7 OE21 68.0 REMARK 620 3 CGU A 26 OE12 82.5 79.4 REMARK 620 4 CGU A 29 OE22 158.2 133.5 102.7 REMARK 620 5 CGU A 29 OE21 143.7 75.9 86.6 58.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 603 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CGU A 7 OE21 REMARK 620 2 CGU A 16 OE12 117.9 REMARK 620 3 CGU A 26 OE11 78.8 65.8 REMARK 620 4 CGU A 29 OE21 70.2 161.7 102.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 606 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CGU A 20 OE12 REMARK 620 2 CGU A 20 OE22 69.5 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NL1 RELATED DB: PDB REMARK 900 BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION REMARK 900 RELATED ID: 4NZQ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE COORDS CONTAIN DELETION OF RESIDUES 146-167, CORRESPONDING TO REMARK 999 UNP RESIDUES 189-210 DBREF 4O03 A 1 145 UNP P00734 THRB_HUMAN 44 188 DBREF 4O03 A 168 579 UNP P00734 THRB_HUMAN 211 622 SEQRES 1 A 557 ALA ASN THR PHE LEU CGU CGU VAL ARG LYS GLY ASN LEU SEQRES 2 A 557 CGU ARG CGU CYS VAL CGU CGU THR CYS SER TYR CGU CGU SEQRES 3 A 557 ALA PHE CGU ALA LEU CGU SER SER THR ALA THR ASP VAL SEQRES 4 A 557 PHE TRP ALA LYS TYR THR ALA CYS GLU THR ALA ARG THR SEQRES 5 A 557 PRO ARG ASP LYS LEU ALA ALA CYS LEU GLU GLY ASN CYS SEQRES 6 A 557 ALA GLU GLY LEU GLY THR ASN TYR ARG GLY HIS VAL ASN SEQRES 7 A 557 ILE THR ARG SER GLY ILE GLU CYS GLN LEU TRP ARG SER SEQRES 8 A 557 ARG TYR PRO HIS LYS PRO GLU ILE ASN SER THR THR HIS SEQRES 9 A 557 PRO GLY ALA ASP LEU GLN GLU ASN PHE CYS ARG ASN PRO SEQRES 10 A 557 ASP SER SER THR THR GLY PRO TRP CYS TYR THR THR ASP SEQRES 11 A 557 PRO THR VAL ARG ARG GLN GLU CYS SER ILE PRO VAL CYS SEQRES 12 A 557 GLY GLN GLU GLN CYS VAL PRO ASP ARG GLY GLN GLN TYR SEQRES 13 A 557 GLN GLY ARG LEU ALA VAL THR THR HIS GLY LEU PRO CYS SEQRES 14 A 557 LEU ALA TRP ALA SER ALA GLN ALA LYS ALA LEU SER LYS SEQRES 15 A 557 HIS GLN ASP PHE ASN SER ALA VAL GLN LEU VAL GLU ASN SEQRES 16 A 557 PHE CYS ARG ASN PRO ASP GLY ASP GLU GLU GLY VAL TRP SEQRES 17 A 557 CYS TYR VAL ALA GLY LYS PRO GLY ASP PHE GLY TYR CYS SEQRES 18 A 557 ASP LEU ASN TYR CYS GLU GLU ALA VAL GLU GLU GLU THR SEQRES 19 A 557 GLY ASP GLY LEU ASP GLU ASP SER ASP ARG ALA ILE GLU SEQRES 20 A 557 GLY ARG THR ALA THR SER GLU TYR GLN THR PHE PHE ASN SEQRES 21 A 557 PRO ARG THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU SEQRES 22 A 557 ARG PRO LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR SEQRES 23 A 557 GLU ARG GLU LEU LEU GLU SER TYR ILE ASP GLY ARG ILE SEQRES 24 A 557 VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO TRP SEQRES 25 A 557 GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU LEU SEQRES 26 A 557 CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU THR SEQRES 27 A 557 ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS ASN SEQRES 28 A 557 PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS HIS SEQRES 29 A 557 SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SER SEQRES 30 A 557 MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN TRP SEQRES 31 A 557 ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS LEU SEQRES 32 A 557 LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO VAL SEQRES 33 A 557 CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU GLN SEQRES 34 A 557 ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN LEU SEQRES 35 A 557 LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN PRO SEQRES 36 A 557 SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU ARG SEQRES 37 A 557 PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR ASP SEQRES 38 A 557 ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY LYS SEQRES 39 A 557 ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO PHE SEQRES 40 A 557 VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN MET SEQRES 41 A 557 GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP GLY SEQRES 42 A 557 LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS LYS SEQRES 43 A 557 TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU MODRES 4O03 ASN A 100 ASN GLYCOSYLATION SITE MODRES 4O03 ASN A 78 ASN GLYCOSYLATION SITE MODRES 4O03 ASN A 373 ASN GLYCOSYLATION SITE MODRES 4O03 CGU A 6 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 7 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 14 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 16 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 19 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 20 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 25 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 26 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 29 GLU GAMMA-CARBOXY-GLUTAMIC ACID MODRES 4O03 CGU A 32 GLU GAMMA-CARBOXY-GLUTAMIC ACID 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 CA A 602 1 HET CA A 603 1 HET CA A 604 1 HET CA A 605 1 HET CA A 606 1 HET NAG A 701 14 HET NAG A 702 14 HET NAG A 703 14 HETNAM CGU GAMMA-CARBOXY-GLUTAMIC ACID HETNAM CA CALCIUM ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 CA 5(CA 2+) FORMUL 7 NAG 3(C8 H15 N O6) HELIX 1 1 ASN A 12 VAL A 18 1 7 HELIX 2 2 SER A 23 LEU A 31 1 9 HELIX 3 3 PHE A 40 ALA A 46 1 7 HELIX 4 4 PRO A 53 GLU A 62 1 10 HELIX 5 5 PRO A 172 GLN A 176 5 5 HELIX 6 6 ALA A 251 GLU A 255 5 5 HELIX 7 7 GLU A 309 GLU A 314 1 6 HELIX 8 8 PRO A 368 ASP A 371 5 4 HELIX 9 9 ASP A 442 GLY A 453 1 12 HELIX 10 10 GLY A 462 THR A 469 1 8 HELIX 11 11 GLU A 489 ASP A 495 1 7 HELIX 12 12 LEU A 566 GLN A 576 1 11 SHEET 1 A 3 CYS A 86 GLN A 87 0 SHEET 2 A 3 TRP A 125 THR A 128 -1 O TYR A 127 N GLN A 87 SHEET 3 A 3 ARG A 135 GLU A 137 -1 O GLN A 136 N CYS A 126 SHEET 1 B 2 CYS A 231 TYR A 232 0 SHEET 2 B 2 PHE A 240 GLY A 241 -1 O GLY A 241 N CYS A 231 SHEET 1 C 7 SER A 325 ASP A 326 0 SHEET 2 C 7 GLN A 481 PRO A 486 -1 O VAL A 482 N SER A 325 SHEET 3 C 7 LYS A 455 GLY A 460 -1 N VAL A 458 O VAL A 483 SHEET 4 C 7 PRO A 528 LYS A 532 -1 O VAL A 530 N ARG A 457 SHEET 5 C 7 TRP A 539 VAL A 545 -1 O MET A 542 N PHE A 529 SHEET 6 C 7 GLY A 558 HIS A 562 -1 O THR A 561 N ILE A 544 SHEET 7 C 7 MET A 505 ALA A 508 -1 N PHE A 506 O TYR A 560 SHEET 1 D 7 GLN A 335 ARG A 340 0 SHEET 2 D 7 GLU A 345 LEU A 352 -1 O GLU A 345 N ARG A 340 SHEET 3 D 7 TRP A 357 THR A 360 -1 O LEU A 359 N SER A 351 SHEET 4 D 7 ALA A 421 LEU A 425 -1 O MET A 423 N VAL A 358 SHEET 5 D 7 LYS A 397 ILE A 406 -1 N TYR A 405 O LEU A 422 SHEET 6 D 7 LEU A 379 ILE A 383 -1 N ILE A 383 O LYS A 397 SHEET 7 D 7 GLN A 335 ARG A 340 -1 N PHE A 339 O LEU A 380 SHEET 1 E 2 LEU A 366 TYR A 367 0 SHEET 2 E 2 LYS A 372 ASN A 373 -1 O LYS A 372 N TYR A 367 SSBOND 1 CYS A 17 CYS A 22 1555 1555 2.03 SSBOND 2 CYS A 47 CYS A 60 1555 1555 2.07 SSBOND 3 CYS A 65 CYS A 143 1555 1555 2.07 SSBOND 4 CYS A 86 CYS A 126 1555 1555 2.04 SSBOND 5 CYS A 114 CYS A 138 1555 1555 2.03 SSBOND 6 CYS A 170 CYS A 248 1555 1555 2.05 SSBOND 7 CYS A 191 CYS A 231 1555 1555 2.02 SSBOND 8 CYS A 219 CYS A 243 1555 1555 2.04 SSBOND 9 CYS A 293 CYS A 439 1555 1555 2.05 SSBOND 10 CYS A 348 CYS A 364 1555 1555 2.02 SSBOND 11 CYS A 493 CYS A 507 1555 1555 2.06 SSBOND 12 CYS A 521 CYS A 551 1555 1555 2.08 LINK C LEU A 5 N CGU A 6 1555 1555 1.50 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 1.34 LINK C CGU A 14 N ARG A 15 1555 1555 1.33 LINK C ARG A 15 N CGU A 16 1555 1555 1.32 LINK C CGU A 16 N CYS A 17 1555 1555 1.34 LINK C VAL A 18 N CGU A 19 1555 1555 1.33 LINK C CGU A 19 N CGU A 20 1555 1555 1.34 LINK C CGU A 20 N THR A 21 1555 1555 1.24 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 1.34 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 A 702 1555 1555 1.46 LINK ND2 ASN A 100 C1 NAG A 703 1555 1555 1.44 LINK ND2 ASN A 373 C1 NAG A 701 1555 1555 1.47 LINK O ALA A 1 CA CA A 604 1555 1555 2.28 LINK OE11 CGU A 6 CA CA A 604 1555 1555 2.29 LINK OE12 CGU A 6 CA CA A 605 1555 1555 2.42 LINK OE12 CGU A 7 CA CA A 602 1555 1555 2.41 LINK OE21 CGU A 7 CA CA A 602 1555 1555 2.50 LINK OE21 CGU A 7 CA CA A 603 1555 1555 2.81 LINK OE22 CGU A 7 CA CA A 604 1555 1555 2.81 LINK OE12 CGU A 16 CA CA A 603 1555 1555 2.73 LINK OE21 CGU A 16 CA CA A 604 1555 1555 2.40 LINK OE22 CGU A 16 CA CA A 604 1555 1555 3.15 LINK OE22 CGU A 16 CA CA A 605 1555 1555 2.26 LINK OE21 CGU A 16 CA CA A 605 1555 1555 2.73 LINK OE12 CGU A 20 CA CA A 605 1555 1555 2.97 LINK OE12 CGU A 20 CA CA A 606 1555 1555 2.22 LINK OE22 CGU A 20 CA CA A 606 1555 1555 2.58 LINK OE12 CGU A 26 CA CA A 602 1555 1555 2.35 LINK OE11 CGU A 26 CA CA A 603 1555 1555 2.17 LINK OE11 CGU A 26 CA CA A 604 1555 1555 3.08 LINK OE22 CGU A 26 CA CA A 604 1555 1555 3.08 LINK OE22 CGU A 29 CA CA A 602 1555 1555 2.11 LINK OE21 CGU A 29 CA CA A 602 1555 1555 2.38 LINK OE21 CGU A 29 CA CA A 603 1555 1555 2.37 CISPEP 1 TYR A 93 PRO A 94 0 -2.32 CISPEP 2 SER A 342 PRO A 343 0 -7.90 CRYST1 177.459 89.431 87.982 90.00 116.36 90.00 C 1 2 1 4 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 0.005635 0.000000 0.002792 0.00000 SCALE2 0.000000 0.011182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012685 0.00000