HEADER HYDROLASE/INHIBITOR 11-APR-05 2BOH
TITLE CRYSTAL STRUCTURE OF FACTOR XA IN COMPLEX WITH COMPOUND "1"
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: COAGULATION FACTOR XA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: LIGHT CHAIN, RESIDUES 126-234;
COMPND 5 SYNONYM: STUART FACTOR, STUART-PROWER FACTOR;
COMPND 6 EC: 3.4.21.6;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: COAGULATION FACTOR XA;
COMPND 9 CHAIN: B;
COMPND 10 FRAGMENT: LIGHT CHAIN, RESIDUES 235-488;
COMPND 11 SYNONYM: STUART FACTOR, STUART-PROWER FACTOR;
COMPND 12 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 TISSUE: BLOOD;
SOURCE 6 MOL_ID: 2;
SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 8 ORGANISM_COMMON: HUMAN;
SOURCE 9 ORGANISM_TAXID: 9606;
SOURCE 10 TISSUE: BLOOD
KEYWDS HYDROLASE/INHIBITOR, COMPLEX (HYDROLASE-INHIBITOR), PROTEIN-INHIBITOR
KEYWDS 2 COMPLEX, BLOOD COAGULATION FACTOR, SERINE PROTEINASE, RATIONAL DRUG
KEYWDS 3 DESIGN, CALCIUM-BINDING, EGF-LIKE DOMAIN, GAMMA-CARBOXYGLUTAMIC
KEYWDS 4 ACID, GLYCOPROTEIN, HYDROLASE, HYDROXYLATION, PLASMA, POLYMORPHISM,
KEYWDS 5 PROTEASE, SERINE PROTEASE, VITAMIN K, ZYMOGEN, HYDROLASE-INHIBITOR
KEYWDS 6 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.NAZARE,D.W.WILL,H.MATTER,H.SCHREUDER,K.RITTER,M.URMANN,M.ESSRICH,
AUTHOR 2 A.BAUER,M.WAGNER,J.CZECH,V.LAUX,V.WEHNER
REVDAT 6 13-NOV-24 2BOH 1 REMARK
REVDAT 5 13-DEC-23 2BOH 1 REMARK LINK
REVDAT 4 30-JAN-19 2BOH 1 REMARK
REVDAT 3 29-JAN-14 2BOH 1 TITLE REMARK VERSN HETSYN
REVDAT 3 2 1 FORMUL
REVDAT 2 24-FEB-09 2BOH 1 VERSN
REVDAT 1 05-APR-06 2BOH 0
JRNL AUTH M.NAZARE,D.W.WILL,H.MATTER,H.SCHREUDER,K.RITTER,M.URMANN,
JRNL AUTH 2 M.ESSRICH,A.BAUER,M.WAGNER,J.CZECH,M.LORENZ,V.LAUX,V.WEHNER
JRNL TITL PROBING THE SUBPOCKETS OF FACTOR XA REVEALS TWO BINDING
JRNL TITL 2 MODES FOR INHIBITORS BASED ON A 2-CARBOXYINDOLE SCAFFOLD: A
JRNL TITL 3 STUDY COMBINING STRUCTURE-ACTIVITY RELATIONSHIP AND X-RAY
JRNL TITL 4 CRYSTALLOGRAPHY.
JRNL REF J.MED.CHEM. V. 48 4511 2005
JRNL REFN ISSN 0022-2623
JRNL PMID 15999990
JRNL DOI 10.1021/JM0490540
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNX 2000
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) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 16670
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) : 0.207
REMARK 3 R VALUE (WORKING SET) : 0.207
REMARK 3 FREE R VALUE : 0.253
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100
REMARK 3 FREE R VALUE TEST SET COUNT : 685
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
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) : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 13
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2524
REMARK 3 BIN FREE R VALUE : 0.2376
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.40
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2249
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 34
REMARK 3 SOLVENT ATOMS : 221
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 41.30
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 8.24400
REMARK 3 B22 (A**2) : 2.91000
REMARK 3 B33 (A**2) : -11.15300
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) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.008
REMARK 3 BOND ANGLES (DEGREES) : 1.511
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.20
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750
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) : 1.250 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.270 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.450 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.310 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : MASK
REMARK 3 KSOL : 0.37
REMARK 3 BSOL : 54.27
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.PARAM
REMARK 3 PARAMETER FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 1 : AVENTIS.TOP
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2BOH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-05.
REMARK 100 THE DEPOSITION ID IS D_1290023601.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-JUN-01
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 5.70
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-4
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9340
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16670
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 200 DATA REDUNDANCY : 4.400
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4
REMARK 200 DATA REDUNDANCY IN SHELL : 4.40
REMARK 200 R MERGE FOR SHELL (I) : 0.31000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNX
REMARK 200 STARTING MODEL: PDB ENTRY 1LPG
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG600, MES, CACL2, PH 5.7, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0 K, PH 5.70
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 28.05000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.60000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.10000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.60000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.05000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.10000
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2760 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13500 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 400
REMARK 400 COMPOUND
REMARK 400 FUNCTION: FACTOR XA CONVERTS PROTHROMBIN TO THROMBIN
REMARK 400 DURING BLOOD CLOTTING
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 -83
REMARK 465 GLU A -82
REMARK 465 MET A -81
REMARK 465 LYS A -80
REMARK 465 LYS A -79
REMARK 465 GLY A -78
REMARK 465 HIS A -77
REMARK 465 LEU A -76
REMARK 465 GLU A -75
REMARK 465 ARG A -74
REMARK 465 GLU A -73
REMARK 465 CYS A -72
REMARK 465 MET A -71
REMARK 465 GLU A -70
REMARK 465 GLU A -69
REMARK 465 THR A -68
REMARK 465 CYS A -67
REMARK 465 SER A -66
REMARK 465 TYR A -65
REMARK 465 GLU A -64
REMARK 465 GLU A -63
REMARK 465 ALA A -62
REMARK 465 ARG A -61
REMARK 465 GLU A -60
REMARK 465 VAL A -59
REMARK 465 PHE A -58
REMARK 465 GLU A -57
REMARK 465 ASP A -56
REMARK 465 SER A -55
REMARK 465 ASP A -54
REMARK 465 LYS A -53
REMARK 465 THR A -52
REMARK 465 ASN A -51
REMARK 465 GLU A -50
REMARK 465 PHE A -49
REMARK 465 TRP A -48
REMARK 465 ASN A -47
REMARK 465 LYS A -46
REMARK 465 TYR A -45
REMARK 465 LYS A -44
REMARK 465 ASP A -43
REMARK 465 GLY A -42
REMARK 465 ASP A -41
REMARK 465 GLN A -40
REMARK 465 CYS A -39
REMARK 465 GLU A -38
REMARK 465 THR A -37
REMARK 465 SER A -36
REMARK 465 PRO A -35
REMARK 465 CYS A -34
REMARK 465 GLN A -33
REMARK 465 ASN A -32
REMARK 465 GLN A -31
REMARK 465 GLY A -30
REMARK 465 LYS A -29
REMARK 465 CYS A -28
REMARK 465 LYS A -27
REMARK 465 ASP A -26
REMARK 465 GLY A -25
REMARK 465 LEU A -24
REMARK 465 GLY A -23
REMARK 465 GLU A -22
REMARK 465 TYR A -21
REMARK 465 THR A -20
REMARK 465 CYS A -19
REMARK 465 THR A -18
REMARK 465 CYS A -17
REMARK 465 LEU A -16
REMARK 465 GLU A -15
REMARK 465 GLY A -14
REMARK 465 PHE A -13
REMARK 465 GLU A -12
REMARK 465 GLY A -11
REMARK 465 LYS A -10
REMARK 465 ASN A -9
REMARK 465 CYS A -8
REMARK 465 GLU A -7
REMARK 465 LEU A -6
REMARK 465 PHE A -5
REMARK 465 THR A -4
REMARK 465 GLY B 246
REMARK 465 LEU B 247
REMARK 465 PRO B 248
REMARK 465 LYS B 249
REMARK 465 ALA B 250
REMARK 465 LYS B 251
REMARK 465 SER B 252
REMARK 465 HIS B 253
REMARK 465 ALA B 254
REMARK 465 PRO B 255
REMARK 465 GLU B 256
REMARK 465 VAL B 257
REMARK 465 ILE B 258
REMARK 465 THR B 259
REMARK 465 SER B 260
REMARK 465 SER B 261
REMARK 465 PRO B 262
REMARK 465 LEU B 263
REMARK 465 LYS B 264
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 51 CA C O CB CG CD NE
REMARK 470 ARG A 51 CZ NH1 NH2
REMARK 470 ARG B 245 CA C O CB CG CD NE
REMARK 470 ARG B 245 CZ NH1 NH2
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 GLU B 77 N - CA - C ANGL. DEV. = -16.4 DEGREES
REMARK 500 CYS B 182 CA - CB - SG ANGL. DEV. = 6.7 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 LYS A -2 -70.64 -110.41
REMARK 500 LEU A -1 -103.67 -96.60
REMARK 500 GLN A 10 -115.12 -131.23
REMARK 500 ASN A 17 162.24 67.42
REMARK 500 SER A 18 150.32 78.35
REMARK 500 LYS A 34 -49.63 -134.01
REMARK 500 SER B 48 -176.61 -171.59
REMARK 500 GLU B 74 51.40 -115.64
REMARK 500 GLN B 75 150.79 178.68
REMARK 500 ARG B 115 -166.94 -168.41
REMARK 500 THR B 244 -75.46 -142.50
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 500 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 70 OD1
REMARK 620 2 ASN B 72 O 85.2
REMARK 620 3 GLN B 75 O 152.7 72.9
REMARK 620 4 GLU B 80 OE2 121.3 153.1 82.8
REMARK 620 5 HOH B2045 O 89.3 91.0 106.7 84.9
REMARK 620 6 HOH B2046 O 79.6 87.5 83.4 101.3 168.9
REMARK 620 N 1 2 3 4 5
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: DSSP
REMARK 700 THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS
REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY
REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
REMARK 700 ARE IDENTICAL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 500
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IIA B 1
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1C5M RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING,
REMARK 900 SUB- MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR
REMARK 900 RELATED ID: 1EZQ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH
REMARK 900 RPR128515
REMARK 900 RELATED ID: 1F0R RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH
REMARK 900 RPR208815
REMARK 900 RELATED ID: 1F0S RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH
REMARK 900 RPR208707
REMARK 900 RELATED ID: 1FAX RELATED DB: PDB
REMARK 900 COAGULATION FACTOR XA INHIBITOR COMPLEX
REMARK 900 RELATED ID: 1FJS RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE INHIBITOR ZK-807834 (CI-1031)COMPLEXED
REMARK 900 WITH FACTOR XA
REMARK 900 RELATED ID: 1FXY RELATED DB: PDB
REMARK 900 COAGULATION FACTOR XA-TRYPSIN CHIMERA INHIBITED WITH D-PHE-PRO-ARG-
REMARK 900 CHLOROMETHYLKETONE
REMARK 900 RELATED ID: 1G2L RELATED DB: PDB
REMARK 900 FACTOR XA INHIBITOR COMPLEX
REMARK 900 RELATED ID: 1G2M RELATED DB: PDB
REMARK 900 FACTOR XA INHIBITOR COMPLEX
REMARK 900 RELATED ID: 1HCG RELATED DB: PDB
REMARK 900 BLOOD COAGULATION FACTOR XA
REMARK 900 RELATED ID: 1IOE RELATED DB: PDB
REMARK 900 HUNMAN COAGULATION FACTOR XA COMPLEXD WITH M55532
REMARK 900 RELATED ID: 1IQE RELATED DB: PDB
REMARK 900 HUMAN COAGULATION FACTOR XA COMPLEXD WITH M55590
REMARK 900 RELATED ID: 1IQF RELATED DB: PDB
REMARK 900 HUMAN COAGULATION FACTOR XA COMPLEXD WITH M55165
REMARK 900 RELATED ID: 1IQG RELATED DB: PDB
REMARK 900 HUNMAN COAGULATION FACTOR XA COMPLEXD WITH M55159
REMARK 900 RELATED ID: 1IQH RELATED DB: PDB
REMARK 900 HUNMAN COAGULATION FACTOR XA COMPLEXD WITH M55143
REMARK 900 RELATED ID: 1IQI RELATED DB: PDB
REMARK 900 HUNMAN COAGULATION FACTOR XA COMPLEXD WITH M55125
REMARK 900 RELATED ID: 1IQJ RELATED DB: PDB
REMARK 900 HUNMAN COAGULATION FACTOR XA COMPLEXD WITH M55124
REMARK 900 RELATED ID: 1IQK RELATED DB: PDB
REMARK 900 HUNMAN COAGULATION FACTOR XA COMPLEXD WITH M55113
REMARK 900 RELATED ID: 1IQL RELATED DB: PDB
REMARK 900 HUNMAN COAGULATION FACTOR XA COMPLEXD WITH M54476
REMARK 900 RELATED ID: 1IQM RELATED DB: PDB
REMARK 900 HUNMAN COAGULATION FACTOR XA COMPLEXD WITH M54471
REMARK 900 RELATED ID: 1IQN RELATED DB: PDB
REMARK 900 HUMAN COAGULATION FACTOR XA COMPLEXD WITH M55192
REMARK 900 RELATED ID: 1KSN RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXEDWITH
REMARK 900 FXV673
REMARK 900 RELATED ID: 1KYE RELATED DB: PDB
REMARK 900 FACTOR XA IN COMPLEX WITH (R)-2-(3- ADAMANTAN-1-YL-UREIDO)-3-(3-
REMARK 900 CARBAMIMIDOYL- PHENYL)-N-PHENETHYL-PROPIONAMIDE
REMARK 900 RELATED ID: 1LPG RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 79.
REMARK 900 RELATED ID: 1LPK RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 125.
REMARK 900 RELATED ID: 1LPZ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 41.
REMARK 900 RELATED ID: 1LQD RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 45.
REMARK 900 RELATED ID: 1MQ5 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF 3-CHLORO-N-[4-CHLORO -2-[[(4-CHLOROPHENYL)
REMARK 900 AMINO]CARBONYL]PHENYL]- 4-[(4-METHYL-1-PIPERAZINYL)METHYL]-2-
REMARK 900 THIOPHENECARBOXAMIDE COMPLEXED WITHHUMAN FACTOR XA
REMARK 900 RELATED ID: 1MQ6 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF 3-CHLORO-N-[4-CHLORO -2-[[(5-CHLORO-2-
REMARK 900 PYRIDINYL)AMINO]CARBONYL] -6-METHOXYPHENYL]-4-[[(4,5-DIHYDRO-2-
REMARK 900 OXAZOLYL)METHYLAMINO]METHYL]-2- THIOPHENECARBOXAMIDE COMPLEXED WITH
REMARK 900 HUMAN FACTOR XA
REMARK 900 RELATED ID: 1MSX RELATED DB: PDB
REMARK 900 HUMAN FACTOR XA COMPLEXED WITH 2-[3-(15N- AMINO-15N-IMINO-13C-
REMARK 900 METHYL)PHENOXY]-6-[3 -(15N-AMINO-13C-METHYL)PHENOXY]-3,5- DIFLUORO-
REMARK 900 4-METHYLPYRIDINE (ZK-806299), BINDING MODELFROM DOUBLE REDOR NMR
REMARK 900 AND MD SIMULATIONS.
REMARK 900 RELATED ID: 1NFU RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXEDWITH
REMARK 900 RPR132747
REMARK 900 RELATED ID: 1NFW RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXEDWITH
REMARK 900 RPR209685
REMARK 900 RELATED ID: 1NFX RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXEDWITH
REMARK 900 RPR208944
REMARK 900 RELATED ID: 1NFY RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXEDWITH
REMARK 900 RPR200095
REMARK 900 RELATED ID: 1NL8 RELATED DB: PDB
REMARK 900 THEORETICAL MODEL OF THE TISSUE FACTOR/ FACTOR VIIA/FACTORXA COMPLEX
REMARK 900 RELATED ID: 1P0S RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF BLOOD COAGULATION FACTOR XA IN COMPLEXWITH
REMARK 900 ECOTIN M84R
REMARK 900 RELATED ID: 1V3X RELATED DB: PDB
REMARK 900 FACTOR XA IN COMPLEX WITH THE INHIBITOR 1 -[6-METHYL-4,5,6,7-
REMARK 900 TETRAHYDROTHIAZOLO(5, 4-C)PYRIDIN-2-YL] CARBONYL-2-CARBAMOYL-4 -(6-
REMARK 900 CHLORONAPHTH-2-YLSULPHONYL)PIPERAZINE
REMARK 900 RELATED ID: 1XKA RELATED DB: PDB
REMARK 900 FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S) -(3'-
REMARK 900 AMIDINO-3- BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID
REMARK 900 RELATED ID: 1XKB RELATED DB: PDB
REMARK 900 FACTOR XA COMPLEXED WITH A SYNTHETIC INHIBITOR FX-2212A,(2S) -(3'-
REMARK 900 AMIDINO-3- BIPHENYLYL)-5-(4-PYRIDYLAMINO)PENTANOIC ACID
REMARK 900 RELATED ID: 2BMG RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF FACTOR XA IN COMPLEX WITH 50
DBREF 2BOH A -83 51 UNP P00742 FA10_HUMAN 126 234
DBREF 2BOH B 16 264 UNP P00742 FA10_HUMAN 235 488
SEQRES 1 A 134 GLU GLU MET LYS LYS GLY HIS LEU GLU ARG GLU CYS MET
SEQRES 2 A 134 GLU GLU THR CYS SER TYR GLU GLU ALA ARG GLU VAL PHE
SEQRES 3 A 134 GLU ASP SER ASP LYS THR ASN GLU PHE TRP ASN LYS TYR
SEQRES 4 A 134 LYS ASP GLY ASP GLN CYS GLU THR SER PRO CYS GLN ASN
SEQRES 5 A 134 GLN GLY LYS CYS LYS ASP GLY LEU GLY GLU TYR THR CYS
SEQRES 6 A 134 THR CYS LEU GLU GLY PHE GLU GLY LYS ASN CYS GLU LEU
SEQRES 7 A 134 PHE THR ARG LYS LEU CYS SER LEU ASP ASN GLY ASP CYS
SEQRES 8 A 134 ASP GLN PHE CYS HIS GLU GLU GLN ASN SER VAL VAL CYS
SEQRES 9 A 134 SER CYS ALA ARG GLY TYR THR LEU ALA ASP ASN GLY LYS
SEQRES 10 A 134 ALA CYS ILE PRO THR GLY PRO TYR PRO CYS GLY LYS GLN
SEQRES 11 A 134 THR LEU GLU ARG
SEQRES 1 B 254 ILE VAL GLY GLY GLN GLU CYS LYS ASP GLY GLU CYS PRO
SEQRES 2 B 254 TRP GLN ALA LEU LEU ILE ASN GLU GLU ASN GLU GLY PHE
SEQRES 3 B 254 CYS GLY GLY THR ILE LEU SER GLU PHE TYR ILE LEU THR
SEQRES 4 B 254 ALA ALA HIS CYS LEU TYR GLN ALA LYS ARG PHE LYS VAL
SEQRES 5 B 254 ARG VAL GLY ASP ARG ASN THR GLU GLN GLU GLU GLY GLY
SEQRES 6 B 254 GLU ALA VAL HIS GLU VAL GLU VAL VAL ILE LYS HIS ASN
SEQRES 7 B 254 ARG PHE THR LYS GLU THR TYR ASP PHE ASP ILE ALA VAL
SEQRES 8 B 254 LEU ARG LEU LYS THR PRO ILE THR PHE ARG MET ASN VAL
SEQRES 9 B 254 ALA PRO ALA CYS LEU PRO GLU ARG ASP TRP ALA GLU SER
SEQRES 10 B 254 THR LEU MET THR GLN LYS THR GLY ILE VAL SER GLY PHE
SEQRES 11 B 254 GLY ARG THR HIS GLU LYS GLY ARG GLN SER THR ARG LEU
SEQRES 12 B 254 LYS MET LEU GLU VAL PRO TYR VAL ASP ARG ASN SER CYS
SEQRES 13 B 254 LYS LEU SER SER SER PHE ILE ILE THR GLN ASN MET PHE
SEQRES 14 B 254 CYS ALA GLY TYR ASP THR LYS GLN GLU ASP ALA CYS GLN
SEQRES 15 B 254 GLY ASP SER GLY GLY PRO HIS VAL THR ARG PHE LYS ASP
SEQRES 16 B 254 THR TYR PHE VAL THR GLY ILE VAL SER TRP GLY GLU GLY
SEQRES 17 B 254 CYS ALA ARG LYS GLY LYS TYR GLY ILE TYR THR LYS VAL
SEQRES 18 B 254 THR ALA PHE LEU LYS TRP ILE ASP ARG SER MET LYS THR
SEQRES 19 B 254 ARG GLY LEU PRO LYS ALA LYS SER HIS ALA PRO GLU VAL
SEQRES 20 B 254 ILE THR SER SER PRO LEU LYS
HET CA A 500 1
HET IIA B 1 33
HETNAM CA CALCIUM ION
HETNAM IIA 1-{[5-(5-CHLORO-2-THIENYL)ISOXAZOL-3-YL]METHYL}-N-(1-
HETNAM 2 IIA ISOPROPYLPIPERIDIN-4-YL)-1H-INDOLE-2-CARBOXAMIDE
FORMUL 3 CA CA 2+
FORMUL 4 IIA C25 H27 CL N4 O2 S
FORMUL 5 HOH *221(H2 O)
HELIX 1 1 LEU A 3 CYS A 8 5 6
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 THR B 244 1 11
SHEET 1 AA 2 PHE A 11 GLU A 14 0
SHEET 2 AA 2 VAL A 19 SER A 22 -1 O VAL A 20 N HIS A 13
SHEET 1 AB 2 TYR A 27 LEU A 29 0
SHEET 2 AB 2 CYS A 36 PRO A 38 -1 O ILE A 37 N THR A 28
SHEET 1 BA 7 GLN B 20 GLU B 21 0
SHEET 2 BA 7 LYS B 156 PRO B 161 -1 O MET B 157 N GLN B 20
SHEET 3 BA 7 THR B 135 GLY B 140 -1 O GLY B 136 N VAL B 160
SHEET 4 BA 7 PRO B 198 PHE B 203 -1 O PRO B 198 N SER B 139
SHEET 5 BA 7 THR B 206 TRP B 215 -1 O THR B 206 N PHE B 203
SHEET 6 BA 7 GLY B 226 LYS B 230 -1 O ILE B 227 N TRP B 215
SHEET 7 BA 7 MET B 180 ALA B 183 -1 O PHE B 181 N TYR B 228
SHEET 1 BB 7 GLN B 30 ASN B 35 0
SHEET 2 BB 7 GLY B 40 ILE B 46 -1 N PHE B 41 O LEU B 33
SHEET 3 BB 7 TYR B 51 THR B 54 -1 O LEU B 53 N THR B 45
SHEET 4 BB 7 ALA B 104 LEU B 108 -1 O ALA B 104 N THR B 54
SHEET 5 BB 7 ALA B 81 LYS B 90 -1 N GLU B 86 O ARG B 107
SHEET 6 BB 7 PHE B 64 VAL B 68 -1 O PHE B 64 N VAL B 85
SHEET 7 BB 7 GLN B 30 ASN B 35 -1 O LEU B 32 N ARG B 67
SSBOND 1 CYS A 1 CYS A 12 1555 1555 2.04
SSBOND 2 CYS A 8 CYS A 21 1555 1555 2.03
SSBOND 3 CYS A 23 CYS A 36 1555 1555 2.03
SSBOND 4 CYS A 44 CYS B 122 1555 1555 2.03
SSBOND 5 CYS B 22 CYS B 27 1555 1555 2.04
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 2.02
LINK CA CA A 500 OD1 ASP B 70 1555 1555 2.56
LINK CA CA A 500 O ASN B 72 1555 1555 2.70
LINK CA CA A 500 O GLN B 75 1555 1555 2.53
LINK CA CA A 500 OE2 GLU B 80 1555 1555 2.61
LINK CA CA A 500 O HOH B2045 1555 1555 2.88
LINK CA CA A 500 O HOH B2046 1555 1555 2.91
SITE 1 AC1 6 ASP B 70 ASN B 72 GLN B 75 GLU B 80
SITE 2 AC1 6 HOH B2045 HOH B2046
SITE 1 AC2 16 THR B 98 TYR B 99 GLU B 147 PHE B 174
SITE 2 AC2 16 ASP B 189 ALA B 190 GLN B 192 SER B 195
SITE 3 AC2 16 VAL B 213 TRP B 215 GLY B 216 GLY B 219
SITE 4 AC2 16 GLY B 226 ILE B 227 TYR B 228 HOH B2103
CRYST1 56.100 72.200 79.200 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 0.017825 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013850 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012626 0.00000