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Open data
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Basic information
Entry | Database: PDB / ID: 1czt | ||||||
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Title | CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V | ||||||
![]() | PROTEIN (COAGULATION FACTOR V) | ||||||
![]() | BLOOD CLOTTING / COAGULATION / MEMBRANE-BINDING / DISCOIDIN FAMILY / CALCIUM-INDEPENDENT | ||||||
Function / homology | ![]() response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation ...response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / blood coagulation / Platelet degranulation / signaling receptor activity / copper ion binding / endoplasmic reticulum lumen / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Macedo-Ribeiro, S. / Bode, W. / Huber, R. / Kane, W.H. / Fuentes-Prior, P. | ||||||
![]() | ![]() Title: Crystal structures of the membrane-binding C2 domain of human coagulation factor V. Authors: Macedo-Ribeiro, S. / Bode, W. / Huber, R. / Quinn-Allen, M.A. / Kim, S.W. / Ortel, T.L. / Bourenkov, G.P. / Bartunik, H.D. / Stubbs, M.T. / Kane, W.H. / Fuentes-Prior, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.4 KB | Display | ![]() |
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PDB format | ![]() | 32.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 364.6 KB | Display | ![]() |
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Full document | ![]() | 366 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1czsSC ![]() 1czvC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 18611.420 Da / Num. of mol.: 1 / Fragment: C2 DISCOIDIN-LIKE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 10.2 Details: AMMONIUM SULFATE, pH 10.20, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 7, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→26.73 Å / Num. obs: 13815 / % possible obs: 94 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 1.87→1.9 Å / Rmerge(I) obs: 0.287 / % possible all: 86.8 |
Reflection shell | *PLUS % possible obs: 86.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CZS Resolution: 1.87→8 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.87→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |