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- PDB-2ra0: X-ray Structure of FXa in complex with 7-fluoroindazole -

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Basic information

Entry
Database: PDB / ID: 2ra0
TitleX-ray Structure of FXa in complex with 7-fluoroindazole
Components(Coagulation factor XFactor X) x 2
KeywordsHYDROLASE / serine protease / Blood coagulation / Calcium / Cleavage on pair of basic residues / EGF-like domain / Gamma-carboxyglutamic acid / Glycoprotein / Hydroxylation / Polymorphism / Zymogen
Function / homology
Function and homology information


coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-JNJ / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsAbad, M.C.
CitationJournal: J.Med.Chem. / Year: 2008
Title: 7-fluoroindazoles as potent and selective inhibitors of factor xa.
Authors: Lee, Y.K. / Parks, D.J. / Lu, T. / Thieu, T.V. / Markotan, T. / Pan, W. / McComsey, D.F. / Milkiewicz, K.L. / Crysler, C.S. / Ninan, N. / Abad, M.C. / Giardino, E.C. / Maryanoff, B.E. / ...Authors: Lee, Y.K. / Parks, D.J. / Lu, T. / Thieu, T.V. / Markotan, T. / Pan, W. / McComsey, D.F. / Milkiewicz, K.L. / Crysler, C.S. / Ninan, N. / Abad, M.C. / Giardino, E.C. / Maryanoff, B.E. / Damiano, B.P. / Player, M.R.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor X
L: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4223
Polymers31,8932
Non-polymers5291
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.871, 74.984, 75.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor X / Factor X / Stuart factor / Stuart-Prower factor


Mass: 26447.104 Da / Num. of mol.: 1 / Fragment: heavy chain, UNP residues 235-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Mammalian / Gene: F10 / Plasmid: pcep4 / Strain (production host): HEK293ebna / References: UniProt: P00742, coagulation factor Xa
#2: Protein Coagulation factor X / Factor X / Stuart factor / Stuart-Prower factor


Mass: 5446.028 Da / Num. of mol.: 1 / Fragment: light chain, UNP residues 128-178 / Mutation: L88V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Mammalian / Gene: F10 / Plasmid: pcep4 / Strain (production host): HEK293ebna / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-JNJ / 1-(3-amino-1,2-benzisoxazol-5-yl)-6-(4-{2-[(dimethylamino)methyl]-1H-imidazol-1-yl}-2-fluorophenyl)-7-fluoro-1H-indazole-3-carboxamide / 1-(3-Aminobenzo[d]isoxazol-5-yl)-6-[4-(2-dimethylaminomethylimidazol-1-yl)-2-fluorophenyl]-7-fluoro-1H-indazole-3-carboxylic Acid Amide


Mass: 528.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H22F2N8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20%Peg 3350, 10mM CaCl2, 0.1M Tris-maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Apr 15, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→74 Å / Num. obs: 12708 / % possible obs: 99.51 % / Redundancy: 7.05 % / Rsym value: 0.107 / Net I/σ(I): 29.305
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.92 % / Rmerge(I) obs: 0.0713 / Mean I/σ(I) obs: 2.07 / Num. unique all: 1282 / Rsym value: 0.245 / % possible all: 98.55

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Processing

Software
NameVersionClassificationNB
SAINTV7.03Adata scaling
CNSrefinement
PDB_EXTRACT3data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
CNSphasing
RefinementResolution: 2.3→53.06 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.314 1303 10.2 %
Rwork0.246 --
obs-12612 98.7 %
Displacement parametersBiso mean: 37.238 Å2
Baniso -1Baniso -2Baniso -3
1-9.061 Å20 Å20 Å2
2--9.614 Å20 Å2
3----18.675 Å2
Refinement stepCycle: LAST / Resolution: 2.3→53.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 39 81 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4871.5
X-RAY DIFFRACTIONc_scbond_it1.8042
X-RAY DIFFRACTIONc_mcangle_it2.5162
X-RAY DIFFRACTIONc_scangle_it2.6342.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2inh.par
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param

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