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Yorodumi- PDB-1nfu: CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nfu | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH RPR132747 | ||||||
Components |
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Keywords | HYDROLASE | ||||||
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 / external side of plasma membrane / endoplasmic reticulum lumen / 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: 2.05 Å | ||||||
Authors | Maignan, S. / Guilloteau, J.P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2003 Title: Molecular structures of human Factor Xa complexed with ketopiperazine inhibitors: preference for a neutral group in the S1 pocket. Authors: Maignan, S. / Guilloteau, J.P. / Choi-Sledeski, Y.M. / Becker, M.R. / Ewing, W.R. / Pauls, H.W. / Spada, A.P. / Mikol, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nfu.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nfu.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nfu ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nfu | HTTPS FTP |
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-Related structure data
Related structure data | 1nfwC 1nfxC 1nfyC 1fosS 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: 28550.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Blood / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa |
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#2: Protein | Mass: 21919.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Blood / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-RRP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 18-20% PEG 600, 50MM MES-NAOH,1MM RPR132747, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 19 ℃ / pH: 6 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→26 Å / Num. all: 18808 / Num. obs: 18808 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.032 |
Reflection | *PLUS Redundancy: 2.4 % |
Reflection shell | *PLUS % possible obs: 89.4 % / Rmerge(I) obs: 0.118 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FOS Resolution: 2.05→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: refinement of the structure was performed without r-free calculation
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Displacement parameters | Biso mean: 29.7 Å2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refinement | *PLUS | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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