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- PDB-1nfw: CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nfw | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN COAGULATION FACTOR XA COMPLEXED WITH RPR209685 | ||||||
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![]() | HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maignan, S. / Guilloteau, J.P. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.1 KB | Display | ![]() |
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PDB format | ![]() | 54.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1nfuC ![]() 1nfxC ![]() 1nfyC ![]() 1ezqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() |
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#2: Protein | Mass: 15210.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Blood / Source: (natural) ![]() |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-RRR / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.04 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 18-20% PEG 600, 50MM MES-NAOH,1MM RPR209685, pH 5.70 , VAPOR DIFFUSION, HANGING DROP, temperature 292 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
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: 2.1→20 Å / Num. all: 19181 / Num. obs: 18587 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.058 |
Reflection | *PLUS Redundancy: 2.3 % |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.147 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EZQ Resolution: 2.1→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: 27 Å2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS |