PDB Short entry for 1YGC HEADER HYDROLASE 04-JAN-05 1YGC TITLE SHORT FACTOR VIIA WITH A SMALL MOLECULE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR VII; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: HEAVY CHAIN (RESIDUES 213-466); COMPND 5 SYNONYM: SERUM PROTHROMBIN CONVERSION ACCELERATOR, SPCA, COMPND 6 PROCONVERTIN, EPTACOG ALFA; COMPND 7 EC: 3.4.21.21; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: COAGULATION FACTOR VII; COMPND 11 CHAIN: L; COMPND 12 FRAGMENT: LIGHT CHAIN, DEL 1-149 FROM FULL LENGTH COMPND 13 (RESIDUES 150-212); COMPND 14 SYNONYM: SERUM PROTHROMBIN CONVERSION ACCELERATOR, SPCA, COMPND 15 PROCONVERTIN, EPTACOG ALFA; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F7; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HIGH FIVE; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: VIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: GP67SSFVII; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: F7; SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 18 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: HIGH FIVE; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: VIRUS; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: GP67SSFVII KEYWDS INVERTED OXY-ANION HOLE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.G.OLIVERO,C.EIGENBROT,R.GOLDSMITH,K.ROBARGE,D.R.ARTIS, AUTHOR 2 J.FLYGARE,T.RAWSON,C.REFINO,S.BUNTING,D.KIRCHHOFER REVDAT 3 24-FEB-09 1YGC 1 VERSN REVDAT 2 13-DEC-05 1YGC 1 JRNL REVDAT 1 18-JAN-05 1YGC 0 JRNL AUTH A.G.OLIVERO,C.EIGENBROT,R.GOLDSMITH,K.ROBARGE, JRNL AUTH 2 D.R.ARTIS,J.FLYGARE,T.RAWSON,D.P.SUTHERLIN, JRNL AUTH 3 S.KADKHODAYAN,M.BERESINI,L.O.ELLIOTT,G.G.DEGUZMAN, JRNL AUTH 4 D.W.BANNER,M.ULTSCH,U.MARZEC,S.R.HANSON,C.REFINO, JRNL AUTH 5 S.BUNTING,D.KIRCHHOFER JRNL TITL A SELECTIVE, SLOW BINDING INHIBITOR OF FACTOR VIIA JRNL TITL 2 BINDS TO A NONSTANDARD ACTIVE SITE CONFORMATION JRNL TITL 3 AND ATTENUATES THROMBUS FORMATION IN VIVO. JRNL REF J.BIOL.CHEM. V. 280 9160 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15632123 JRNL DOI 10.1074/JBC.M409068200 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2000.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,MOLECULAR REMARK 3 : SIMULATIONS (BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2203986.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 34943 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 878 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 34943 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5598 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 0.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 49 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2368 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.32000 REMARK 3 B22 (A**2) : -1.32000 REMARK 3 B33 (A**2) : 2.64000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.08 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.26 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.270 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.860 ; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.220 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.350 ; 6.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 47.74 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PARWAT.PRO REMARK 3 PARAMETER FILE 3 : PARAM.CALCIUM REMARK 3 PARAMETER FILE 4 : 905.PAR REMARK 3 PARAMETER FILE 5 : PARAM.SO4 REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : TOPWAT.PRO REMARK 3 TOPOLOGY FILE 3 : TOP.CALCIUM REMARK 3 TOPOLOGY FILE 4 : 905.TOP REMARK 3 TOPOLOGY FILE 5 : TOP.SO4 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YGC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031482. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34943 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.3000 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 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, GLYCEROL, PEG REMARK 280 400, CALCIUM ION, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K 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 58.16000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.61000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.08000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.61000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.61000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.24000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.61000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.61000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.08000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.61000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.61000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 87.24000 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 58.16000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -252.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 116.32000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA H 538 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS L 143 REMARK 465 ARG L 144 REMARK 465 ASN L 145 REMARK 465 ALA L 146 REMARK 465 SER L 147 REMARK 465 LYS L 148 REMARK 465 PRO L 149 REMARK 465 GLN L 150 REMARK 465 GLY L 151 REMARK 465 ARG L 152 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 LYS H 170D REMARK 475 GLY L 107 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG H 84 NE CZ NH1 NH2 REMARK 480 GLN H 170 CG CD OE1 NE2 REMARK 480 THR L 108 CB OG1 CG2 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 H 68 CA - CB - CG ANGL. DEV. = -13.9 DEGREES REMARK 500 HIS H 199 N - CA - C ANGL. DEV. = -16.4 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 HIS H 71 -62.21 -142.32 REMARK 500 THR H 129C -54.33 -125.58 REMARK 500 GLN L 100 -105.48 -121.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H 553 DISTANCE = 5.70 ANGSTROMS REMARK 525 HOH H 613 DISTANCE = 6.60 ANGSTROMS 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 H 300 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH H 541 O REMARK 620 2 GLU H 75 O 106.0 REMARK 620 3 ASP H 72 O 85.2 78.8 REMARK 620 4 GLU H 70 OE1 86.6 161.3 88.7 REMARK 620 5 GLU H 80 OE2 90.2 90.2 166.4 103.8 REMARK 620 6 HOH H 454 O 168.0 86.0 97.7 81.8 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA H 538 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH H 438 O REMARK 620 2 HOH H 553 O 94.6 REMARK 620 3 HOH H 553 O 118.1 125.1 REMARK 620 4 HOH H 438 O 106.3 118.3 94.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 300 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA H 538 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 301 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 302 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 304 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 308 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 310 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 311 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 312 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 905 H 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JBU RELATED DB: PDB REMARK 900 SHORT FACTOR VII ZYMOGEN WITH INHIBITORY PEPTIDE A183 REMARK 900 RELATED ID: 1KLI RELATED DB: PDB REMARK 900 SHORT FACTOR VIIA WITH BENZAMIDINE REMARK 900 RELATED ID: 1KLJ RELATED DB: PDB REMARK 900 SHORT FACTOR VIIA UNINHIBITED REMARK 900 RELATED ID: 1DAN RELATED DB: PDB REMARK 900 FACTOR VIIA COMPLEX WITH TISSUE FACTOR DBREF 1YGC H 16 257 UNP P08709 FA7_HUMAN 213 466 DBREF 1YGC L 90 152 UNP P08709 FA7_HUMAN 150 212 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 L 63 ILE CYS VAL ASN GLU ASN GLY GLY CYS GLU GLN TYR CYS SEQRES 2 L 63 SER ASP HIS THR GLY THR LYS ARG SER CYS ARG CYS HIS SEQRES 3 L 63 GLU GLY TYR SER LEU LEU ALA ASP GLY VAL SER CYS THR SEQRES 4 L 63 PRO THR VAL GLU TYR PRO CYS GLY LYS ILE PRO ILE LEU SEQRES 5 L 63 GLU LYS ARG ASN ALA SER LYS PRO GLN GLY ARG HET CA H 300 1 HET CA H 538 1 HET SO4 H 301 5 HET SO4 L 302 5 HET SO4 H 304 5 HET SO4 H 308 5 HET SO4 H 310 5 HET SO4 H 311 5 HET SO4 H 312 5 HET 905 H 1 38 HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM 905 (R)-4-[2-(3-AMINO-BENZENESULFONYLAMINO)-1-(3,5- HETNAM 2 905 DIETHOXY-2-FLUOROPHENYL)-2-OXO-ETHYLAMINO]-2-HYDROXY- HETNAM 3 905 BENZAMIDINE FORMUL 3 CA 2(CA 2+) FORMUL 5 SO4 7(O4 S 2-) FORMUL 12 905 C25 H28 F N5 O6 S FORMUL 13 HOH *260(H2 O) HELIX 1 1 ALA H 55 ASP H 60 5 6 HELIX 2 2 ASN H 60D ARG H 62 5 3 HELIX 3 3 GLU H 125 THR H 129C 1 8 HELIX 4 4 LEU H 129D VAL H 129G 5 4 HELIX 5 5 MET H 164 SER H 170B 1 9 HELIX 6 6 CYS H 191 SER H 195 5 5 HELIX 7 7 TYR H 234 ARG H 243 1 10 HELIX 8 8 ASN L 93 CYS L 98 5 6 SHEET 1 A 8 LYS H 20 VAL H 21 0 SHEET 2 A 8 MET H 156 LEU H 163 -1 O VAL H 157 N LYS H 20 SHEET 3 A 8 MET H 180 ALA H 183 -1 O CYS H 182 N LEU H 163 SHEET 4 A 8 GLY H 226 ARG H 230 -1 O TYR H 228 N PHE H 181 SHEET 5 A 8 THR H 206 TRP H 215 -1 N TRP H 215 O VAL H 227 SHEET 6 A 8 PRO H 198 TYR H 203 -1 N THR H 201 O TYR H 208 SHEET 7 A 8 PHE H 135 GLY H 140 -1 N LEU H 137 O ALA H 200 SHEET 8 A 8 MET H 156 LEU H 163 -1 O VAL H 160 N SER H 136 SHEET 1 B 8 LEU H 251 ALA H 254 0 SHEET 2 B 8 GLN H 81 PRO H 91 1 N VAL H 88 O LEU H 252 SHEET 3 B 8 ALA H 104 LEU H 108 -1 O LEU H 105 N ILE H 89 SHEET 4 B 8 TRP H 51 SER H 54 -1 N VAL H 52 O LEU H 106 SHEET 5 B 8 ALA H 39 LEU H 46 -1 N THR H 45 O VAL H 53 SHEET 6 B 8 GLN H 30 VAL H 35 -1 N LEU H 33 O CYS H 42 SHEET 7 B 8 LEU H 64 LEU H 68 -1 O ILE H 65 N LEU H 34 SHEET 8 B 8 GLN H 81 PRO H 91 -1 O GLN H 81 N LEU H 68 SHEET 1 C 2 TYR L 101 ASP L 104 0 SHEET 2 C 2 ARG L 110 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 SSBOND 1 CYS H 22 CYS H 27 1555 1555 2.04 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.04 SSBOND 3 CYS H 122 CYS L 135 1555 1555 2.02 SSBOND 4 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 5 CYS H 191 CYS H 220 1555 1555 2.03 SSBOND 6 CYS L 91 CYS L 102 1555 1555 2.04 SSBOND 7 CYS L 98 CYS L 112 1555 1555 2.03 SSBOND 8 CYS L 114 CYS L 127 1555 1555 2.03 LINK CA CA H 300 O HOH H 541 1555 1555 2.51 LINK CA CA H 300 O GLU H 75 1555 1555 2.32 LINK CA CA H 300 O ASP H 72 1555 1555 2.45 LINK CA CA H 300 OE1 GLU H 70 1555 1555 2.43 LINK CA CA H 300 OE2 GLU H 80 1555 1555 2.45 LINK CA CA H 300 O HOH H 454 1555 1555 2.45 LINK CA CA H 538 O HOH H 438 1555 1555 2.87 LINK CA CA H 538 O HOH H 553 1555 1555 2.74 LINK CA CA H 538 O HOH H 553 1555 7556 2.74 LINK CA CA H 538 O HOH H 438 1555 7556 2.87 CISPEP 1 PHE H 256 PRO H 257 0 0.18 SITE 1 AC1 6 GLU H 70 ASP H 72 GLU H 75 GLU H 80 SITE 2 AC1 6 HOH H 454 HOH H 541 SITE 1 AC2 2 HOH H 438 HOH H 553 SITE 1 AC3 7 MET H 164 THR H 165 ARG H 230 HOH H 537 SITE 2 AC3 7 HOH H 612 HOH H 720 HOH H 789 SITE 1 AC4 4 ARG H 129B SER L 103 ASP L 104 HOH L 447 SITE 1 AC5 4 SER H 244 GLU H 245 HOH H 562 HOH L 516 SITE 1 AC6 5 SER H 82 ARG H 83 ARG H 84 HIS H 109 SITE 2 AC6 5 GLN H 110 SITE 1 AC7 4 THR H 98 THR H 99 PRO H 170I HOH H 605 SITE 1 AC8 6 SER H 170B GLN H 217 HIS H 224 PHE H 225 SITE 2 AC8 6 VAL H 227 HOH H 634 SITE 1 AC9 5 THR H 115 ASP H 116 HIS H 117 HOH H 621 SITE 2 AC9 5 TYR L 133 SITE 1 BC1 19 HIS H 57 ASP H 60 THR H 98 ASP H 102 SITE 2 BC1 19 ASP H 189 SER H 190 LYS H 192 SER H 195 SITE 3 BC1 19 SER H 214 TRP H 215 GLY H 216 GLY H 219 SITE 4 BC1 19 CYS H 220 GLY H 226 HOH H 449 HOH H 463 SITE 5 BC1 19 HOH H 536 HOH H 867 HOH H1013 CRYST1 95.220 95.220 116.320 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 0.010502 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008597 0.00000