HEADER HYDROLASE/HYDROLASE INHIBITOR 18-AUG-11 3TH3 TITLE MG2+ IS REQUIRED FOR OPTIMAL FOLDING OF THE GAMMA-CARBOXYGLUTAMIC ACID TITLE 2 (GLA) DOMAINS OF VITAMIN K-DEPENDENT CLOTTING FACTORS AT TITLE 3 PHYSIOLOGICAL CA2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR VII LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: COAGULATION FACTOR VII; COMPND 5 SYNONYM: PROCONVERTIN, SERUM PROTHROMBIN CONVERSION ACCELERATOR, COMPND 6 SPCA; COMPND 7 EC: 3.4.21.21; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: COAGULATION FACTOR VII HEAVY CHAIN; COMPND 10 CHAIN: H; COMPND 11 SYNONYM: PROCONVERTIN, SERUM PROTHROMBIN CONVERSION ACCELERATOR, COMPND 12 SPCA; COMPND 13 EC: 3.4.21.21; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: TISSUE FACTOR; COMPND 16 CHAIN: T; COMPND 17 SYNONYM: TF, COAGULATION FACTOR III, THROMBOPLASTIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: BLOOD; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 OTHER_DETAILS: BLOOD; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 OTHER_DETAILS: BLOOD KEYWDS HYDROLASE, BLOOD CLOTTING, SERINE PROTEASE, BLOOD COAGULATION, KEYWDS 2 SOLUBLE TISSUE FACTOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.VADIVEL,S.AGAH,D.CASCIO,K.PADMANABHAN,S.P.BAJAJ REVDAT 6 06-DEC-23 3TH3 1 REMARK REVDAT 5 13-SEP-23 3TH3 1 HETSYN REVDAT 4 29-JUL-20 3TH3 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 03-OCT-18 3TH3 1 CAVEAT COMPND REMARK LINK REVDAT 3 2 1 ATOM REVDAT 2 24-JAN-18 3TH3 1 JRNL REVDAT 1 22-AUG-12 3TH3 0 JRNL AUTH K.VADIVEL,S.AGAH,A.MESSER,D.CASCIO,M.S.BAJAJ,S.KRISHNASWAMY, JRNL AUTH 2 C.T.ESMON,K.PADMANABHAN,S.P.BAJAJ JRNL TITL MG2+ IS REQUIRED FOR OPTIMAL FOLDING OF THE JRNL TITL 2 GAMMA-CARBOXYGLUTAMIC ACID (GLA) DOMAINS OF VITAMIN JRNL TITL 3 K-DEPENDENT CLOTTING FACTORS AT PHYSIOLOGICAL CA2+ JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 21733 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1184 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1388 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.3810 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.4050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3934 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 83 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 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): 0.358 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 : 0.910 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.849 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4100 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5583 ; 1.850 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 497 ; 7.450 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;34.103 ;24.056 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 657 ;21.821 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;15.934 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 623 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3092 ; 0.009 ; 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): 2502 ; 0.830 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4058 ; 1.596 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1598 ; 2.172 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1525 ; 3.654 ; 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 3TH3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067469. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22917 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 55.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : 9.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2A2Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 50 MM TRIS-HCL, 50 MM N REMARK 280 -(2-ACETAMIDO)IMINODIACETIC ACID, 150 MM NACL, 2.5 MM CALCIUM REMARK 280 CHLORIDE, 1.25 MM MAGNESIUM CHLORIDE, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.44700 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, T 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 L 1 REMARK 465 ASN L 2 REMARK 465 ALA L 3 REMARK 465 PHE L 4 REMARK 465 LEU L 5 REMARK 465 CGU L 6 REMARK 465 CGU L 7 REMARK 465 LEU L 8 REMARK 465 ARG L 9 REMARK 465 PRO L 10 REMARK 465 GLY L 11 REMARK 465 SER L 12 REMARK 465 LEU L 13 REMARK 465 CGU L 14 REMARK 465 ARG L 15 REMARK 465 CGU L 16 REMARK 465 CYS L 17 REMARK 465 LYS L 18 REMARK 465 CGU L 19 REMARK 465 CGU L 20 REMARK 465 GLN L 21 REMARK 465 CYS L 22 REMARK 465 SER L 23 REMARK 465 PHE L 24 REMARK 465 CGU L 25 REMARK 465 CGU L 26 REMARK 465 ALA L 27 REMARK 465 ARG L 28 REMARK 465 CGU L 29 REMARK 465 ILE L 30 REMARK 465 PHE L 31 REMARK 465 LYS L 32 REMARK 465 ASP L 33 REMARK 465 ALA L 34 REMARK 465 CGU L 35 REMARK 465 ARG L 36 REMARK 465 THR L 37 REMARK 465 LYS L 38 REMARK 465 LEU L 39 REMARK 465 PHE L 40 REMARK 465 TRP L 41 REMARK 465 ILE L 42 REMARK 465 SER L 43 REMARK 465 TYR L 44 REMARK 465 SER L 45 REMARK 465 ASP L 46 REMARK 465 VAL T 83 REMARK 465 GLU T 84 REMARK 465 SER T 85 REMARK 465 THR T 86 REMARK 465 GLY T 87 REMARK 465 SER T 88 REMARK 465 ALA T 89 REMARK 465 ILE T 113 REMARK 465 GLN T 114 REMARK 465 SER T 115 REMARK 465 PHE T 116 REMARK 465 GLU T 117 REMARK 465 GLN T 118 REMARK 465 VAL T 119 REMARK 465 GLY T 120 REMARK 465 THR T 121 REMARK 465 LYS T 122 REMARK 465 VAL T 123 REMARK 465 ASN T 124 REMARK 465 VAL T 125 REMARK 465 THR T 126 REMARK 465 VAL T 127 REMARK 465 GLU T 128 REMARK 465 ASP T 129 REMARK 465 GLU T 130 REMARK 465 LEU T 155 REMARK 465 TYR T 156 REMARK 465 TYR T 157 REMARK 465 TRP T 158 REMARK 465 LYS T 159 REMARK 465 SER T 160 REMARK 465 SER T 161 REMARK 465 SER T 162 REMARK 465 SER T 163 REMARK 465 GLY T 164 REMARK 465 LYS T 165 REMARK 465 LYS T 166 REMARK 465 THR T 167 REMARK 465 ALA T 168 REMARK 465 PHE T 175 REMARK 465 LEU T 176 REMARK 465 ILE T 177 REMARK 465 ASP T 178 REMARK 465 VAL T 179 REMARK 465 ASP T 180 REMARK 465 LYS T 181 REMARK 465 GLY T 182 REMARK 465 GLU T 183 REMARK 465 ASN T 184 REMARK 465 TYR T 185 REMARK 465 MET T 210 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 OG SER H 195 C2 0GE H 301 1.41 REMARK 500 NE2 HIS H 57 CM 0GE H 301 1.48 REMARK 500 OG SER H 195 CM 0GE H 301 2.04 REMARK 500 CB SER H 195 C2 0GE H 301 2.18 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 GLN L 100 -50.43 -125.07 REMARK 500 THR L 108 147.81 -170.36 REMARK 500 ARG L 110 172.14 -51.90 REMARK 500 GLU L 116 138.19 -37.85 REMARK 500 VAL L 125 -16.83 -140.54 REMARK 500 LYS H 24 123.68 -36.11 REMARK 500 ASN H 37 52.33 33.67 REMARK 500 GLN H 40 135.87 -33.71 REMARK 500 LEU H 41 -70.25 -133.61 REMARK 500 SER H 54 -167.74 -129.46 REMARK 500 ASN H 60D 58.21 -108.34 REMARK 500 HIS H 71 -54.22 -130.27 REMARK 500 ASP H 116 -17.48 -48.78 REMARK 500 ARG H 147 -2.84 80.48 REMARK 500 ASP H 186 24.35 -73.02 REMARK 500 SER H 214 -68.19 -132.21 REMARK 500 PHE T 19 -1.26 84.89 REMARK 500 ASP T 66 84.54 -165.62 REMARK 500 ASN T 138 3.87 82.06 REMARK 500 ASN T 199 59.87 35.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 0GE H 301 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 L 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY L 47 O REMARK 620 2 GLN L 49 OE1 64.7 REMARK 620 3 ASP L 63 OD1 93.9 80.5 REMARK 620 4 ASP L 63 OD2 91.1 120.6 46.1 REMARK 620 5 GLN L 64 O 165.6 127.8 82.3 76.2 REMARK 620 6 HOH L 304 O 70.0 105.5 157.1 115.8 109.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA H 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU H 70 OE2 REMARK 620 2 ASP H 72 O 69.6 REMARK 620 3 GLU H 75 O 145.3 80.6 REMARK 620 4 GLU H 80 OE1 63.4 131.6 137.1 REMARK 620 5 HOH H 419 O 86.4 73.0 67.6 93.0 REMARK 620 6 HOH H 442 O 92.2 88.9 105.0 103.2 161.1 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: N-{[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}-L- REMARK 630 ALPHA-GLUTAMYL-N-[(2S,3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2- REMARK 630 HYDROXYHEXAN-3-YL]GLYCINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0GE H 301 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ANS GLU GLY AR7 0QE REMARK 630 DETAILS: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2A2Q RELATED DB: PDB REMARK 900 COMPLEX OF ACTIVE-SITE INHIBITED HUMAN COAGULATION FACTOR VIIA WITH REMARK 900 HUMAN SOLUBLE TISSUE FACTOR IN THE PRESENCE OF CA2+, MG2+, NA+, AND REMARK 900 ZN2+ REMARK 900 RELATED ID: 3TH2 RELATED DB: PDB REMARK 900 RELATED ID: 3TH4 RELATED DB: PDB DBREF 3TH3 L 1 142 UNP P08709 FA7_HUMAN 61 202 DBREF 3TH3 H 16 257 UNP P08709 FA7_HUMAN 213 466 DBREF 3TH3 T 6 210 UNP P13726 TF_HUMAN 38 242 SEQRES 1 L 142 ALA ASN ALA PHE LEU CGU CGU LEU ARG PRO GLY SER LEU SEQRES 2 L 142 CGU ARG CGU CYS LYS CGU CGU GLN CYS SER PHE CGU CGU SEQRES 3 L 142 ALA ARG CGU ILE PHE LYS ASP ALA CGU ARG THR LYS LEU SEQRES 4 L 142 PHE TRP ILE SER TYR SER ASP GLY ASP GLN CYS ALA SER SEQRES 5 L 142 SER PRO CYS GLN ASN GLY GLY SER CYS LYS ASP GLN LEU SEQRES 6 L 142 GLN SER TYR ILE CYS PHE CYS LEU PRO ALA PHE GLU GLY SEQRES 7 L 142 ARG ASN CYS GLU THR HIS LYS ASP ASP GLN LEU ILE CYS SEQRES 8 L 142 VAL ASN GLU ASN GLY GLY CYS GLU GLN TYR CYS SER ASP SEQRES 9 L 142 HIS THR GLY THR LYS ARG SER CYS ARG CYS HIS GLU GLY SEQRES 10 L 142 TYR SER LEU LEU ALA ASP GLY VAL SER CYS THR PRO THR SEQRES 11 L 142 VAL GLU TYR PRO CYS GLY LYS ILE PRO ILE LEU GLU SEQRES 1 H 254 ILE VAL GLY GLY LYS VAL CYS PRO LYS GLY GLU CYS PRO SEQRES 2 H 254 TRP GLN VAL LEU LEU LEU VAL ASN GLY ALA GLN LEU CYS SEQRES 3 H 254 GLY GLY THR LEU ILE ASN THR ILE TRP VAL VAL SER ALA SEQRES 4 H 254 ALA HIS CYS PHE ASP LYS ILE LYS ASN TRP ARG ASN LEU SEQRES 5 H 254 ILE ALA VAL LEU GLY GLU HIS ASP LEU SER GLU HIS ASP SEQRES 6 H 254 GLY ASP GLU GLN SER ARG ARG VAL ALA GLN VAL ILE ILE SEQRES 7 H 254 PRO SER THR TYR VAL PRO GLY THR THR ASN HIS ASP ILE SEQRES 8 H 254 ALA LEU LEU ARG LEU HIS GLN PRO VAL VAL LEU THR ASP SEQRES 9 H 254 HIS VAL VAL PRO LEU CYS LEU PRO GLU ARG THR PHE SER SEQRES 10 H 254 GLU ARG THR LEU ALA PHE VAL ARG PHE SER LEU VAL SER SEQRES 11 H 254 GLY TRP GLY GLN LEU LEU ASP ARG GLY ALA THR ALA LEU SEQRES 12 H 254 GLU LEU MET VAL LEU ASN VAL PRO ARG LEU MET THR GLN SEQRES 13 H 254 ASP CYS LEU GLN GLN SER ARG LYS VAL GLY ASP SER PRO SEQRES 14 H 254 ASN ILE THR GLU TYR MET PHE CYS ALA GLY TYR SER ASP SEQRES 15 H 254 GLY SER LYS ASP SER CYS LYS GLY ASP SER GLY GLY PRO SEQRES 16 H 254 HIS ALA THR HIS TYR ARG GLY THR TRP TYR LEU THR GLY SEQRES 17 H 254 ILE VAL SER TRP GLY GLN GLY CYS ALA THR VAL GLY HIS SEQRES 18 H 254 PHE GLY VAL TYR THR ARG VAL SER GLN TYR ILE GLU TRP SEQRES 19 H 254 LEU GLN LYS LEU MET ARG SER GLU PRO ARG PRO GLY VAL SEQRES 20 H 254 LEU LEU ARG ALA PRO PHE PRO SEQRES 1 T 205 THR VAL ALA ALA TYR ASN LEU THR TRP LYS SER THR ASN SEQRES 2 T 205 PHE LYS THR ILE LEU GLU TRP GLU PRO LYS PRO VAL ASN SEQRES 3 T 205 GLN VAL TYR THR VAL GLN ILE SER THR LYS SER GLY ASP SEQRES 4 T 205 TRP LYS SER LYS CYS PHE TYR THR THR ASP THR GLU CYS SEQRES 5 T 205 ASP LEU THR ASP GLU ILE VAL LYS ASP VAL LYS GLN THR SEQRES 6 T 205 TYR LEU ALA ARG VAL PHE SER TYR PRO ALA GLY ASN VAL SEQRES 7 T 205 GLU SER THR GLY SER ALA GLY GLU PRO LEU TYR GLU ASN SEQRES 8 T 205 SER PRO GLU PHE THR PRO TYR LEU GLU THR ASN LEU GLY SEQRES 9 T 205 GLN PRO THR ILE GLN SER PHE GLU GLN VAL GLY THR LYS SEQRES 10 T 205 VAL ASN VAL THR VAL GLU ASP GLU ARG THR LEU VAL ARG SEQRES 11 T 205 ARG ASN ASN THR PHE LEU SER LEU ARG ASP VAL PHE GLY SEQRES 12 T 205 LYS ASP LEU ILE TYR THR LEU TYR TYR TRP LYS SER SER SEQRES 13 T 205 SER SER GLY LYS LYS THR ALA LYS THR ASN THR ASN GLU SEQRES 14 T 205 PHE LEU ILE ASP VAL ASP LYS GLY GLU ASN TYR CYS PHE SEQRES 15 T 205 SER VAL GLN ALA VAL ILE PRO SER ARG THR VAL ASN ARG SEQRES 16 T 205 LYS SER THR ASP SER PRO VAL GLU CYS MET HET FUC L 201 10 HET CA L 202 1 HET BGC L 203 11 HET 0GE H 301 41 HET CA H 302 1 HET CL H 303 1 HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM 0GE N-{[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}-L-ALPHA- HETNAM 2 0GE GLUTAMYL-N-[(2S,3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2- HETNAM 3 0GE HYDROXYHEXAN-3-YL]GLYCINAMIDE HETNAM CL CHLORIDE ION HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN 0GE 1,5-DANSYL-GLU-GLY-ARG-CHLOROMETHYL KETONE, BOUND FORM FORMUL 4 FUC C6 H12 O5 FORMUL 5 CA 2(CA 2+) FORMUL 6 BGC C6 H12 O6 FORMUL 7 0GE C26 H38 CL N7 O7 S FORMUL 9 CL CL 1- FORMUL 10 HOH *83(H2 O) HELIX 1 1 GLN L 49 SER L 53 5 5 HELIX 2 2 ASN L 93 CYS L 98 5 6 HELIX 3 3 ALA H 55 ASP H 60 5 6 HELIX 4 4 GLU H 125 THR H 129C 1 8 HELIX 5 5 LEU H 129D VAL H 129G 5 4 HELIX 6 6 MET H 164 SER H 170B 1 9 HELIX 7 7 CYS H 191 SER H 195 5 5 HELIX 8 8 TYR H 234 SER H 244 1 11 HELIX 9 9 LEU T 59 LYS T 65 1 7 HELIX 10 10 THR T 101 THR T 106 1 6 HELIX 11 11 SER T 142 GLY T 148 1 7 HELIX 12 12 LYS T 149 LEU T 151 5 3 SHEET 1 A 2 CYS L 61 ASP L 63 0 SHEET 2 A 2 TYR L 68 CYS L 70 -1 O ILE L 69 N LYS L 62 SHEET 1 B 2 PHE L 76 GLU L 77 0 SHEET 2 B 2 THR L 83 HIS L 84 -1 O THR L 83 N GLU L 77 SHEET 1 C 2 TYR L 101 SER L 103 0 SHEET 2 C 2 SER L 111 ARG L 113 -1 O SER L 111 N SER L 103 SHEET 1 D 2 TYR L 118 LEU L 120 0 SHEET 2 D 2 CYS L 127 PRO L 129 -1 O THR L 128 N SER L 119 SHEET 1 E 7 LYS H 20 VAL H 21 0 SHEET 2 E 7 MET H 156 PRO H 161 -1 O VAL H 157 N LYS H 20 SHEET 3 E 7 PHE H 135 GLY H 140 -1 N SER H 136 O VAL H 160 SHEET 4 E 7 PRO H 198 TYR H 203 -1 O ALA H 200 N LEU H 137 SHEET 5 E 7 THR H 206 TRP H 215 -1 O TYR H 208 N THR H 201 SHEET 6 E 7 GLY H 226 ARG H 230 -1 O VAL H 227 N TRP H 215 SHEET 7 E 7 MET H 180 ALA H 183 -1 N ALA H 183 O GLY H 226 SHEET 1 F 8 LEU H 251 ALA H 254 0 SHEET 2 F 8 GLN H 81 PRO H 91 1 N ILE H 90 O LEU H 252 SHEET 3 F 8 ALA H 104 LEU H 108 -1 O LEU H 105 N ILE H 89 SHEET 4 F 8 TRP H 51 SER H 54 -1 N VAL H 52 O LEU H 106 SHEET 5 F 8 ALA H 39 LEU H 46 -1 N THR H 45 O VAL H 53 SHEET 6 F 8 GLN H 30 VAL H 35 -1 N VAL H 35 O ALA H 39 SHEET 7 F 8 LEU H 64 LEU H 68 -1 O VAL H 67 N LEU H 32 SHEET 8 F 8 GLN H 81 PRO H 91 -1 O ARG H 83 N ALA H 66 SHEET 1 G 3 TYR T 10 THR T 17 0 SHEET 2 G 3 LYS T 20 GLU T 26 -1 O GLU T 26 N TYR T 10 SHEET 3 G 3 GLU T 56 ASP T 58 -1 O CYS T 57 N LEU T 23 SHEET 1 H 4 LYS T 46 THR T 52 0 SHEET 2 H 4 GLN T 32 THR T 40 -1 N ILE T 38 O LYS T 46 SHEET 3 H 4 TYR T 71 PRO T 79 -1 O PHE T 76 N THR T 35 SHEET 4 H 4 LEU T 93 ASN T 96 -1 O LEU T 93 N SER T 77 SHEET 1 I 2 ARG T 135 ARG T 136 0 SHEET 2 I 2 THR T 139 PHE T 140 -1 O THR T 139 N ARG T 136 SHEET 1 J 2 ILE T 152 THR T 154 0 SHEET 2 J 2 GLN T 190 VAL T 192 -1 O VAL T 192 N ILE T 152 SSBOND 1 CYS L 50 CYS L 61 1555 1555 2.04 SSBOND 2 CYS L 55 CYS L 70 1555 1555 1.95 SSBOND 3 CYS L 72 CYS L 81 1555 1555 2.06 SSBOND 4 CYS L 91 CYS L 102 1555 1555 2.02 SSBOND 5 CYS L 98 CYS L 112 1555 1555 2.06 SSBOND 6 CYS L 114 CYS L 127 1555 1555 2.08 SSBOND 7 CYS L 135 CYS H 122 1555 1555 2.08 SSBOND 8 CYS H 22 CYS H 27 1555 1555 2.05 SSBOND 9 CYS H 42 CYS H 58 1555 1555 2.03 SSBOND 10 CYS H 168 CYS H 182 1555 1555 2.05 SSBOND 11 CYS H 191 CYS H 220 1555 1555 2.05 SSBOND 12 CYS T 49 CYS T 57 1555 1555 2.10 SSBOND 13 CYS T 186 CYS T 209 1555 1555 2.05 LINK OG SER L 52 C1 BGC L 203 1555 1555 1.45 LINK OG SER L 60 C1 FUC L 201 1555 1555 1.45 LINK O GLY L 47 CA CA L 202 1555 1555 2.58 LINK OE1 GLN L 49 CA CA L 202 1555 1555 2.11 LINK OD1 ASP L 63 CA CA L 202 1555 1555 2.28 LINK OD2 ASP L 63 CA CA L 202 1555 1555 3.04 LINK O GLN L 64 CA CA L 202 1555 1555 2.35 LINK CA CA L 202 O HOH L 304 1555 1555 1.95 LINK OE2 GLU H 70 CA CA H 302 1555 1555 2.34 LINK O ASP H 72 CA CA H 302 1555 1555 2.58 LINK O GLU H 75 CA CA H 302 1555 1555 2.43 LINK OE1 GLU H 80 CA CA H 302 1555 1555 2.30 LINK CA CA H 302 O HOH H 419 1555 1555 2.48 LINK CA CA H 302 O HOH H 442 1555 1555 2.42 CISPEP 1 PHE H 256 PRO H 257 0 1.41 CISPEP 2 GLU T 26 PRO T 27 0 6.32 CRYST1 78.079 68.894 79.153 90.00 91.19 90.00 P 1 21 1 2 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 0.012808 0.000000 0.000266 0.00000 SCALE2 0.000000 0.014515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012636 0.00000