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Open data
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Basic information
Entry | Database: PDB / ID: 6wv4 | |||||||||||||||||||||
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Title | Human VKOR C43S with warfarin | |||||||||||||||||||||
![]() | Vitamin K epoxide reductase Cys43Ser mutant, termini restrained by green fluorescent protein | |||||||||||||||||||||
![]() | OXIDOREDUCTASE / FLUORESCENT PROTEIN / Vitamin K epoxide Reductase (VKOR) / Vitamin K / warfarin / superwarfarin / vitamin K expoxide(KO) / membrane protein | |||||||||||||||||||||
Function / homology | ![]() peptidyl-glutamic acid carboxylation / vitamin-K-epoxide reductase (warfarin-insensitive) activity / Metabolism of vitamin K / vitamin-K-epoxide reductase (warfarin-sensitive) / vitamin-K-epoxide reductase (warfarin-sensitive) activity / vitamin K metabolic process / positive regulation of coagulation / regulation of blood coagulation / quinone binding / : ...peptidyl-glutamic acid carboxylation / vitamin-K-epoxide reductase (warfarin-insensitive) activity / Metabolism of vitamin K / vitamin-K-epoxide reductase (warfarin-sensitive) / vitamin-K-epoxide reductase (warfarin-sensitive) activity / vitamin K metabolic process / positive regulation of coagulation / regulation of blood coagulation / quinone binding / : / xenobiotic metabolic process / bioluminescence / generation of precursor metabolites and energy / bone development / response to organic cyclic compound / blood coagulation / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Liu, S. / Sukumar, N. / Li, W. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation. Authors: Liu, S. / Li, S. / Shen, G. / Sukumar, N. / Krezel, A.M. / Li, W. #1: ![]() Title: Termini restraining of small membrane proteins enables structure determination at atomic resolution Authors: Liu, S. / Li, S. / Yang, Y. / Li, W. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161 KB | Display | ![]() |
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PDB format | ![]() | 124.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764.6 KB | Display | ![]() |
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Full document | ![]() | 769.1 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wv3C ![]() 6wv5C ![]() 6wv6C ![]() 6wv7C ![]() 6wv8C ![]() 6wv9C ![]() 6wvaC ![]() 6wvbC ![]() 6wvhC ![]() 6wviC ![]() 2b3pS 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: 44181.371 Da / Num. of mol.: 1 Fragment: GPF (UNP residues 1-144) + VKOR + GFP (UNP residues 146-231) Mutation: C43S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: gfp, VKORC1, VKOR, MSTP134, MSTP576, UNQ308/PRO351 / Production host: ![]() References: UniProt: A0A059PIQ0, UniProt: Q9BQB6, UniProt: P42212*PLUS, vitamin-K-epoxide reductase (warfarin-sensitive) |
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#2: Chemical | ChemComp-SWF / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.76 % |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase / pH: 6.5 Details: 25-33% PEG400, 185-220 mM potassium formate, 0.1 M MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 17, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.01→49.35 Å / Num. obs: 11474 / % possible obs: 90 % / Redundancy: 4.5 % / Biso Wilson estimate: 13.83 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.272 / Rpim(I) all: 0.143 / Rrim(I) all: 0.309 / Net I/σ(I): 4.6 / Num. measured all: 51175 / Scaling rejects: 22 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2B3P Resolution: 3.012→48.641 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.63 Å2 / Biso mean: 74.4269 Å2 / Biso min: 21.67 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.012→48.641 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 13.8157 Å / Origin y: -16.8792 Å / Origin z: -45.1281 Å
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Refinement TLS group |
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