PDB Short entry for 2P3U HEADER BLOOD CLOTTING 09-MAR-07 2P3U TITLE CRYSTAL STRUCTURE OF HUMAN FACTOR XA COMPLEXED WITH 3-CHLORO-N-(4- TITLE 2 CHLORO-2-{[(5-CHLOROPYRIDIN-2-YL)AMINO]CARBONYL}-6-METHOXYPHENYL)-4- TITLE 3 [(1-METHYL-1H-IMIDAZOL-2-YL)METHYL]THIOPHENE-2-CARBOXAMIDE {PFIZER TITLE 4 320663} COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR X; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EGF-LIKE 2 DOMAIN; COMPND 5 SYNONYM: STUART FACTOR, STUART-PROWER FACTOR; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: COAGULATION FACTOR X; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: CATALYTIC DOMAIN; COMPND 10 SYNONYM: STUART FACTOR, STUART-PROWER FACTOR; COMPND 11 EC: 3.4.21.6 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: EXTRACTED FROM BLOOD; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606 KEYWDS PROTEIN INHIBITOR COMPLEX, COAGULATION COFACTOR, PROTEASE, BLOOD KEYWDS 2 CLOTTING EXPDTA X-RAY DIFFRACTION AUTHOR M.ADLER,M.WHITLOW REVDAT 3 30-AUG-23 2P3U 1 LINK REVDAT 2 24-FEB-09 2P3U 1 VERSN REVDAT 1 11-SEP-07 2P3U 0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.ADLER,M.J.KOCHANNY,Y.BIN,G.RUMENNIK,D.L.LIGHT, REMARK 1 AUTH 2 S.BIANCALANA,M.WHITLOW REMARK 1 TITL CRYSTAL STRUCTURES OF TWO POTENT NONAMIDINE INHIBITORS BOUND REMARK 1 TITL 2 TO FACTOR XA REMARK 1 REF BIOCHEMISTRY V. 41 15514 2002 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.YE,D.O.ARNAIZ,Y.-L.CHOU,B.D.GRIEDEL,R.KARANJAWALA,W.LEE, REMARK 1 AUTH 2 M.M.MORRISSEY,K.L.SACCHI,S.T.SAKATA,K.J.SHAW,S.C.WU,Z.ZHAO, REMARK 1 AUTH 3 M.ADLER,S.CHEESEMAN,W.P.DOLE,J.EWING,R.FITCH,D.LENTZ, REMARK 1 AUTH 4 A.LIANG,D.LIGHT,J.MORSER,J.POST,G.RUMENNIK,B.SUBRAMANYAM, REMARK 1 AUTH 5 M.E.SULLIVAN,R.VERGONA,J.WALTERS,Y.-X.WANG,K.A.WHITE, REMARK 1 AUTH 6 M.WHITLOW,M.J.KOCHANNY REMARK 1 TITL DISCOVERY OF HIGHLY POTENT AND ORALLY AVAILABLE REMARK 1 TITL 2 THIOPHENE-ANTHRANILAMIDE-BASED FACTOR XA INHIBITORS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 3 REMARK 1 AUTH B.YE,D.O.ARNAIZ,Y.-L.CHOU,B.D.GRIEDEL,R.KARANJAWALA,W.LEE, REMARK 1 AUTH 2 M.M.MORRISSEY,K.L.SACCHI,S.T.SAKATA,K.J.SHAW,S.C.WU,Z.ZHAO, REMARK 1 AUTH 3 M.ADLER,S.CHEESEMAN,W.P.DOLE,J.EWING,R.FITCH,D.LENTZ, REMARK 1 AUTH 4 A.LIANG,D.LIGHT,J.MORSER,J.POST,G.RUMENNIK,B.SUBRAMANYAM, REMARK 1 AUTH 5 M.E.SULLIVAN,R.VERGONA,J.WALTERS,Y.-X.WANG,K.A.WHITE, REMARK 1 AUTH 6 M.WHITLOW,M.J.KOCHANNY REMARK 1 TITL SUBSTITUTED THIOPHENE-ANTHRANILAMIDES AS POTENT INHIBITORS REMARK 1 TITL 2 OF HUMAN FACTOR XA REMARK 1 REF BIOORG.MED.CHEM. V. 15 2127 2007 REMARK 1 REFN ISSN 0968-0896 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.J.KOCHANNY,M.ADLER,J.EWING,B.D.GRIEDEL,E.HO,R.KARANJAWALA, REMARK 1 AUTH 2 W.LEE,D.LENTZ,A.M.LIANG,M.M.MORRISSEY,G.B.PHILLIPS,J.POST, REMARK 1 AUTH 3 K.L.SAKATA,B.SUBRAMANYAM,R.VERGONA,J.WALTERS,K.A.WHITE, REMARK 1 AUTH 4 M.WHITLOW,B.YE,Z.ZHAO,K.J.SHAW REMARK 1 TITL STRUCTURE-ACTIVITY RELATIONSHIPS OF SUBSTITUTED REMARK 1 TITL 2 BENZOTHIOPHENE-ANTHRANILAMIDE FACTOR XA INHIBITORS REMARK 1 REF BIOORG.MED.CHEM.LETT. V. 13 507 2003 REMARK 1 REFN ISSN 0960-894X REMARK 1 REFERENCE 5 REMARK 1 AUTH Y.L.CHOU,D.D.DAVEY,K.A.EAGEN,B.D.GRIEDEL,R.KARANJAWALA, REMARK 1 AUTH 2 G.B.PHILLIPS,K.L.SACCHI,K.J.SHAW,S.C.WU,D.LENTZ,A.M.LIANG, REMARK 1 AUTH 3 L.TRINH,M.M.MORRISSEY,M.J.KOCHANNY REMARK 1 TITL PREPARATION, CHARACTERIZATION AND THE CRYSTAL STRUCTURE OF REMARK 1 TITL 2 THE INHIBITOR ZK-807834 (CI-1031) COMPLEXED WITH FACTOR XA REMARK 1 REF BIOCHEMISTRY V. 39 12534 2000 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 6 REMARK 1 AUTH M.ADLER,D.D.DAVEY,G.B.PHILLIPS,S.H.KIM,J.JANCARIK, REMARK 1 AUTH 2 G.RUMENNIK,D.L.LIGHT,M.WHITLOW REMARK 1 TITL CRYSTAL STRUCTURES OF HUMAN FACTOR XA COMPLEXED WITH POTENT REMARK 1 TITL 2 INHIBITORS REMARK 1 REF J.MED.CHEM. V. 43 3226 2000 REMARK 1 REFN ISSN 0022-2623 REMARK 1 REFERENCE 7 REMARK 1 AUTH G.B.PHILLIPS,B.O.BUCKMAN,D.D.DAVEY,K.A.EAGEN,W.J.GUILFORD, REMARK 1 AUTH 2 J.HINCHMAN,E.HO,S.KOOVAKKAT,A.M.LIANG,D.R.LIGHT,R.MOHAN, REMARK 1 AUTH 3 H.P.NG,J.M.POST,K.J.SHAW,D.SMITH,B.SUBRAMANYAM,M.E.SULLIVAN, REMARK 1 AUTH 4 L.TRINH,R.VERGONA,J.WALTERS,K.WHITE,M.WHITLOW,S.WU,W.XU, REMARK 1 AUTH 5 M.M.MORRISSEY REMARK 1 TITL DISCOVERY OF REMARK 1 TITL 2 N-[2-[5-[AMINO(IMINO)METHYL]-2-HYDROXYPHENOXY]-3,5-DIFLUORO- REMARK 1 TITL 3 6-[3-(4,5-DIHYDRO-1-METHYL-1H-IMIDAZOL-2-YL) REMARK 1 TITL 4 PHENOXY]PYRIDIN-4-YL]-N-METHYLGLYCINE (ZK-807834): A POTENT, REMARK 1 TITL 5 SELECTIVE, AND ORALLY ACTIVE INHIBITOR OF THE BLOOD REMARK 1 TITL 6 COAGULATION ENZYME FACTOR XA REMARK 1 REF J.MED.CHEM. V. 41 3557 1998 REMARK 1 REFN ISSN 0022-2623 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1261609.710 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 39893 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1569 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.2120 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2110 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 3.900 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1593 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : 0.0060 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 40430 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) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6211 REMARK 3 BIN R VALUE (WORKING SET) : 0.2511 REMARK 3 BIN FREE R VALUE : 0.2801 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 211 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2220 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.74000 REMARK 3 B22 (A**2) : -5.12000 REMARK 3 B33 (A**2) : 3.37000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.590 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) : 1.650 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.530 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.460 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.690 ; 3.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 62.23 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.P REMARK 3 PARAMETER FILE 2 : WATER_REP.PAR REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : 663.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : 663.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2P3U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-00 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 : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.080 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40439 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1FJS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A THREE-FOLD EXCESS OF 3-CHLORO-4-(2 REMARK 280 -METHYLAMINO-IMIDAZOL-1-YLMETHYL)-THIOPHENE-2-CARBOXYLIC ACID [4- REMARK 280 CHLORO-2-(5-CHLORO-PYRIDIN-2-YLCARBAMOYL)-6-METHOXY-PHENYL]- REMARK 280 AMIDE WAS ADDED TO THE DES-GLA-FACTOR XA. THE PROTEIN WAS THEN REMARK 280 CONCENTRATED TO 12-17 MG/ML. CRYSTALS WERE GROWN USING 2 UL OF REMARK 280 COMPLEX WITH 2 UL OF RESERVOIR CONTAINING 15-21% PEG1500 AND 10 REMARK 280 MM CACL2. 30-40 UL SITTING DROPS CONTAINING SATURATED INHIBITOR REMARK 280 (5 MM) IN 21% PEG1500, 5 MM CACL2, 20 MM NACL, 25 MM TRIS PH 7.5 REMARK 280 (CRYSTAL SOAKING SOLUTION) WERE EQUILIBRATED OVER A 1 ML REMARK 280 RESERVOIR CONTAINING THE CRYSTAL SOAKING SOLUTION FOR 1 TO 2 REMARK 280 DAYS. A SINGLE FACTOR XA CRYSTAL WAS TRANSFERRED USING A MOUNTED REMARK 280 CRYOLOOP INTO ONE OF THESE SITTING DROPS AND ALLOWED TO SOAK FOR REMARK 280 THREE OR MORE DAYS, EVAPORATION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.00700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.32550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.85850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.32550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.00700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.85850 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 300 REMARK: BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC REMARK 300 ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). REMARK 300 FACTOR XA FORMS A COMPLEX WITH FACTOR VA IN REMARK 300 THE PRESENCE OF CALCIUM AND A PHOSPHOLIPID REMARK 300 MEMBRANE TO PRODUCE THE PROTHROMBINASE COMPLEX. REMARK 300 THIS ENTRY CONTAINS THE EPIDERMAL GROWTH FACTOR REMARK 300 LIKE DOMAIN 2(L) AND THE CATALYTIC DOMAIN (A) REMARK 300 OF FACTOR XA IN THE CRYSTALLOGRAPHIC ASYMMETRIC REMARK 300 UNIT. THE COORDINATES DO NOT CONTAIN THE GLA REMARK 300 DOMAIN OR THE EPIDERMAL GROWTH FACTOR LIKE DOMAIN REMARK 300 1 OF FACTOR XA. ALTHOUGH THE ASYMMETRIC UNIT REMARK 300 CONTAINS A FUNCTIONAL PROTEASE, IT DOES HAVE THE REMARK 300 SAME SPECIFICITY AS THE PROTHROMBINASE COMPLEX. REMARK 300 SEE REMARK 350 FOR INFORMATION ON GENERATING THE REMARK 300 BIOLOGICAL MOLECULE(S). REMARK 300 REMARK 300 GENERATING THE BIOMOLECULE REMARK 300 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 300 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 300 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 300 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 300 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 APPLY THE FOLLOWING TO CHAINS: A, L REMARK 300 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 300 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 300 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 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 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 GLU A 138 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 LEU A 88 -117.17 50.80 REMARK 500 GLN A 98 -111.77 -130.01 REMARK 500 LYS A 122 -44.76 -130.46 REMARK 500 LYS B 62 -70.70 -67.91 REMARK 500 ARG B 115 -172.10 -173.84 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 B 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 70 OD2 REMARK 620 2 ASN B 72 O 86.6 REMARK 620 3 GLN B 75 O 168.9 82.8 REMARK 620 4 GLU B 77 OE2 76.4 86.2 99.7 REMARK 620 5 GLU B 80 OE2 98.6 172.9 91.8 90.2 REMARK 620 6 HOH B 795 O 99.3 98.6 85.4 173.4 85.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 185A O REMARK 620 2 TYR B 185 O 81.4 REMARK 620 3 ARG B 222 O 87.6 165.2 REMARK 620 4 LYS B 224 O 116.6 87.3 88.7 REMARK 620 5 HOH B 816 O 172.8 91.4 99.2 61.8 REMARK 620 6 HOH B 961 O 87.8 97.8 91.7 155.6 94.1 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2P3T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FACTOR XA COMPLEXED WITH 3-CHLORO-4-(2- REMARK 900 METHYLAMINO-IMIDAZOL-1-YLMETHYL)-THIOPHENE-2-CARBOXYLIC ACID [4- REMARK 900 CHLORO-2-(5-CHLORO-PYRIDIN-2-YLCARBAMOYL)-6-METHOXY-PHENYL]-AMIDE REMARK 900 RELATED ID: 1MQ5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-CHLORO-N-[4-CHLORO-2-[[(4-CHLOROPHENYL)AMINO] REMARK 900 CARBONYL]PHENYL]-4-[(4-METHYL-1-PIPERAZINYL)METHYL]-2- REMARK 900 THIOPHENECARBOXAMIDE COMPLEXED WITH HUMAN FACTOR XA REMARK 900 RELATED ID: 1MQ6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-CHLORO-N-[4-CHLORO-2-[[(5-CHLORO-2-PYRIDINYL) REMARK 900 AMINO]CARBONYL]-6-METHOXYPHENYL]-4-[[(4,5-DIHYDRO-2-OXAZOLYL) REMARK 900 METHYLAMINO]METHYL]-2-THIOPHENECARBOXAMIDE COMPLEXED WITH HUMAN REMARK 900 FACTOR XA REMARK 900 RELATED ID: 1FJS RELATED DB: PDB REMARK 900 FACTOR XA COMPLEXED TO ZK807834 REMARK 900 RELATED ID: 1EZQ RELATED DB: PDB REMARK 900 FACTOR XA COMPLEXED TO RPR128515 REMARK 900 RELATED ID: 1F0S RELATED DB: PDB REMARK 900 FACTOR XA COMPLEXED TO RPR208707 REMARK 900 RELATED ID: 1F0R RELATED DB: PDB REMARK 900 FACTOR XA COMPLEXED TO RPR208815 DBREF 2P3U A 87 138 UNP P00742 FA10_HUMAN 127 178 DBREF 2P3U B 16 243 UNP P00742 FA10_HUMAN 235 467 SEQRES 1 A 52 LYS LEU CYS SER LEU ASP ASN GLY ASP CYS ASP GLN PHE SEQRES 2 A 52 CYS HIS GLU GLU GLN ASN SER VAL VAL CYS SER CYS ALA SEQRES 3 A 52 ARG GLY TYR THR LEU ALA ASP ASN GLY LYS ALA CYS ILE SEQRES 4 A 52 PRO THR GLY PRO TYR PRO CYS GLY LYS GLN THR LEU GLU SEQRES 1 B 233 ILE VAL GLY GLY GLN GLU CYS LYS ASP GLY GLU CYS PRO SEQRES 2 B 233 TRP GLN ALA LEU LEU ILE ASN GLU GLU ASN GLU GLY PHE SEQRES 3 B 233 CYS GLY GLY THR ILE LEU SER GLU PHE TYR ILE LEU THR SEQRES 4 B 233 ALA ALA HIS CYS LEU TYR GLN ALA LYS ARG PHE LYS VAL SEQRES 5 B 233 ARG VAL GLY ASP ARG ASN THR GLU GLN GLU GLU GLY GLY SEQRES 6 B 233 GLU ALA VAL HIS GLU VAL GLU VAL VAL ILE LYS HIS ASN SEQRES 7 B 233 ARG PHE THR LYS GLU THR TYR ASP PHE ASP ILE ALA VAL SEQRES 8 B 233 LEU ARG LEU LYS THR PRO ILE THR PHE ARG MET ASN VAL SEQRES 9 B 233 ALA PRO ALA CYS LEU PRO GLU ARG ASP TRP ALA GLU SER SEQRES 10 B 233 THR LEU MET THR GLN LYS THR GLY ILE VAL SER GLY PHE SEQRES 11 B 233 GLY ARG THR HIS GLU LYS GLY ARG GLN SER THR ARG LEU SEQRES 12 B 233 LYS MET LEU GLU VAL PRO TYR VAL ASP ARG ASN SER CYS SEQRES 13 B 233 LYS LEU SER SER SER PHE ILE ILE THR GLN ASN MET PHE SEQRES 14 B 233 CYS ALA GLY TYR ASP THR LYS GLN GLU ASP ALA CYS GLN SEQRES 15 B 233 GLY ASP SER GLY GLY PRO HIS VAL THR ARG PHE LYS ASP SEQRES 16 B 233 THR TYR PHE VAL THR GLY ILE VAL SER TRP GLY GLU GLY SEQRES 17 B 233 CYS ALA ARG LYS GLY LYS TYR GLY ILE TYR THR LYS VAL SEQRES 18 B 233 THR ALA PHE LEU LYS TRP ILE ASP ARG SER MET LYS HET CA B 501 1 HET CA B 502 1 HET 663 B 500 35 HETNAM CA CALCIUM ION HETNAM 663 3-CHLORO-N-(4-CHLORO-2-{[(5-CHLOROPYRIDIN-2-YL) HETNAM 2 663 AMINO]CARBONYL}-6-METHOXYPHENYL)-4-[(1-METHYL-1H- HETNAM 3 663 IMIDAZOL-2-YL)METHYL]THIOPHENE-2-CARBOXAMIDE FORMUL 3 CA 2(CA 2+) FORMUL 5 663 C23 H18 CL3 N5 O3 S FORMUL 6 HOH *267(H2 O) HELIX 1 1 LYS A 87 CYS A 96 5 10 HELIX 2 2 ALA B 55 GLN B 61 5 7 HELIX 3 3 GLU B 124A LEU B 131A 1 9 HELIX 4 4 ASP B 164 SER B 172 1 9 HELIX 5 5 PHE B 234 MET B 242 1 9 SHEET 1 A 2 PHE A 99 GLU A 103 0 SHEET 2 A 2 SER A 106 SER A 110 -1 O SER A 106 N GLU A 103 SHEET 1 B 2 TYR A 115 LEU A 117 0 SHEET 2 B 2 CYS A 124 PRO A 126 -1 O ILE A 125 N THR A 116 SHEET 1 C 7 GLN B 20 GLU B 21 0 SHEET 2 C 7 LYS B 156 PRO B 161 -1 O MET B 157 N GLN B 20 SHEET 3 C 7 THR B 135 GLY B 140 -1 N GLY B 136 O VAL B 160 SHEET 4 C 7 PRO B 198 PHE B 203 -1 O VAL B 200 N ILE B 137 SHEET 5 C 7 THR B 206 TRP B 215 -1 O THR B 210 N HIS B 199 SHEET 6 C 7 GLY B 226 LYS B 230 -1 O ILE B 227 N TRP B 215 SHEET 7 C 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 D 7 GLN B 30 ILE B 34 0 SHEET 2 D 7 GLY B 40 ILE B 46 -1 O CYS B 42 N LEU B 33 SHEET 3 D 7 TYR B 51 THR B 54 -1 O LEU B 53 N THR B 45 SHEET 4 D 7 ALA B 104 LEU B 108 -1 O LEU B 106 N ILE B 52 SHEET 5 D 7 ALA B 81 LYS B 90 -1 N ILE B 89 O VAL B 105 SHEET 6 D 7 LYS B 65 VAL B 68 -1 N VAL B 66 O HIS B 83 SHEET 7 D 7 GLN B 30 ILE B 34 -1 N LEU B 32 O ARG B 67 SSBOND 1 CYS A 89 CYS A 100 1555 1555 2.03 SSBOND 2 CYS A 96 CYS A 109 1555 1555 2.03 SSBOND 3 CYS A 111 CYS A 124 1555 1555 2.04 SSBOND 4 CYS A 132 CYS B 122 1555 1555 2.03 SSBOND 5 CYS B 22 CYS B 27 1555 1555 2.03 SSBOND 6 CYS B 42 CYS B 58 1555 1555 2.03 SSBOND 7 CYS B 168 CYS B 182 1555 1555 2.02 SSBOND 8 CYS B 191 CYS B 220 1555 1555 2.03 LINK OD2 ASP B 70 CA CA B 501 1555 1555 2.32 LINK O ASN B 72 CA CA B 501 1555 1555 2.25 LINK O GLN B 75 CA CA B 501 1555 1555 2.14 LINK OE2 GLU B 77 CA CA B 501 1555 1555 2.36 LINK OE2 GLU B 80 CA CA B 501 1555 1555 2.29 LINK O ASP B 185A CA CA B 502 1555 1555 2.60 LINK O TYR B 185 CA CA B 502 1555 1555 2.38 LINK O ARG B 222 CA CA B 502 1555 1555 2.37 LINK O LYS B 224 CA CA B 502 1555 1555 2.37 LINK CA CA B 501 O HOH B 795 1555 1555 2.23 LINK CA CA B 502 O HOH B 816 1555 1555 2.87 LINK CA CA B 502 O HOH B 961 1555 1555 2.35 CRYST1 56.014 71.717 78.651 90.00 90.00 90.00 P 21 21 21 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 0.017853 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012714 0.00000