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Yorodumi- PDB-3kqe: Factor xa in complex with the inhibitor 3-methyl-1-(3-(5- oxo-4,5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kqe | ||||||
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Title | Factor xa in complex with the inhibitor 3-methyl-1-(3-(5- oxo-4,5-dihydro-1h-1,2,4-triazol-3-yl)phenyl)-6-(2'- (pyrrolidin-1-ylmethyl)biphenyl-4-yl)-5,6-dihydro-1h- pyrazolo[3,4-c]pyridin-7(4h)-one | ||||||
Components |
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Keywords | HYDROLASE / GLYCOPROTEIN / SERINE PROTEASE / PLASMA / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / CALCIUM- BINDING / BLOOD COAGULATION / CALCIUM / PROTEASE / SECRETED / EGF-like domain / Gamma-carboxyglutamic acid | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Sheriff, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Phenyltriazolinones as potent factor Xa inhibitors. Authors: Quan, M.L. / Pinto, D.J. / Rossi, K.A. / Sheriff, S. / Alexander, R.S. / Amparo, E. / Kish, K. / Knabb, R.M. / Luettgen, J.M. / Morin, P. / Smallwood, A. / Woerner, F.J. / Wexler, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kqe.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kqe.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/3kqe ftp://data.pdbj.org/pub/pdb/validation_reports/kq/3kqe | HTTPS FTP |
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-Related structure data
Related structure data | 3ffgSC 3kqbC 3kqcC 3kqdC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26447.104 Da / Num. of mol.: 1 / Fragment: residues 235-468 of factor X uncleaved sequence / Source method: isolated from a natural source / Details: PROTEOLYTIC CLEAVAGE PRODUCT / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa | ||||
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#2: Protein | Mass: 5589.234 Da / Num. of mol.: 1 / Fragment: residues 127-178 of factor X uncleaved sequence / Source method: isolated from a natural source / Details: PROTEOLYTIC CLEAVAGE PRODUCT / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa | ||||
#3: Chemical | ChemComp-LGM / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE MATERIAL IS PROTEOLYTIC CLEAVAGE PRODUCT. IT IS DIFFICULT TO KNOW EXACTLY ...AUTHORS STATE THAT THE MATERIAL IS PROTEOLYTI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 200 mM NaOAc (pH 5.5), 18% PEG 6000, pH 5.500000, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 13775 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.213 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 3.1 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB entry 3FFG, FACTOR XA Resolution: 2.35→36.1 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 116.87 Å2 / Biso mean: 42.057 Å2 / Biso min: 17.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→36.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.54 Å / Total num. of bins used: 7
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