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- PDB-6wv7: Human VKOR with Chlorophacinone -

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Basic information

Entry
Database: PDB / ID: 6wv7
TitleHuman VKOR with Chlorophacinone
ComponentsVitamin K epoxide reductase, termini restrained by green fluorescent protein
KeywordsOXIDOREDUCTASE / FLUORESCENT PROTEIN / Vitamin K epoxide Reductase (VKOR) / Vitamin K / warfarin / superwarfarin / vitamin K expoxide(KO) / Chlorophacinone / membrane protein
Function / homology
Function and homology information


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 ...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 / blood coagulation / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Vitamin K epoxide reductase complex subunit 1 / VKOR domain / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein ...Vitamin K epoxide reductase complex subunit 1 / VKOR domain / Vitamin K epoxide reductase / VKOR domain superfamily / Vitamin K epoxide reductase family / VKc / de novo design (two linked rop proteins) / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chlorophacinone / Green fluorescent protein / Green fluorescent protein / Vitamin K epoxide reductase complex subunit 1
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.483 Å
AuthorsLiu, S. / Sukumar, N. / Li, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL121718 United States
Other privateForefront of Science Award United States
Other privateMCII 2020-854 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R21 EY028705 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM131008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: Science / Year: 2021
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.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
B: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1454
Polymers88,3952
Non-polymers7502
Water3,657203
1
A: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5722
Polymers44,1971
Non-polymers3751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5722
Polymers44,1971
Non-polymers3751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.564, 82.567, 78.782
Angle α, β, γ (deg.)93.390, 97.360, 104.210
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 296 or (resid 297...
21(chain B and (resid 2 through 33 or (resid 34...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLNGLN(chain A and (resid 2 through 296 or (resid 297...AA2 - 2962 - 294
12GLUGLUGLUGLU(chain A and (resid 2 through 296 or (resid 297...AA297295
13SERSERHISHIS(chain A and (resid 2 through 296 or (resid 297...AA2 - 3842 - 382
14SERSERHISHIS(chain A and (resid 2 through 296 or (resid 297...AA2 - 3842 - 382
15SERSERHISHIS(chain A and (resid 2 through 296 or (resid 297...AA2 - 3842 - 382
16SERSERHISHIS(chain A and (resid 2 through 296 or (resid 297...AA2 - 3842 - 382
21SERSERGLYGLY(chain B and (resid 2 through 33 or (resid 34...BB2 - 332 - 33
22GLUGLUGLUGLU(chain B and (resid 2 through 33 or (resid 34...BB3434
23SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390
24SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390
25SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390
26SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390
27SERSERHISHIS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3922 - 390

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Components

#1: Protein Vitamin K epoxide reductase, termini restrained by green fluorescent protein / Vitamin K1 2 / 3-epoxide reductase subunit 1


Mass: 44197.434 Da / Num. of mol.: 2
Fragment: GPF (UNP residues 1-144) + VKOR + GFP (UNP residues 146-231)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: gfp, VKORC1, VKOR, MSTP134, MSTP576, UNQ308/PRO351 / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A059PIQ0, UniProt: Q9BQB6, UniProt: P42212*PLUS, vitamin-K-epoxide reductase (warfarin-sensitive)
#2: Chemical ChemComp-UAJ / Chlorophacinone / 2-[(2R)-2-(4-chlorophenyl)-2-phenylacetyl]-1H-indene-1,3(2H)-dione


Mass: 374.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H15ClO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: anticoagulant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6.5
Details: 33% PEG400, 5% DMSO, 0.1 M sodium acetate, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.483→50 Å / Num. obs: 31278 / % possible obs: 87.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.087 / Rrim(I) all: 0.123 / Χ2: 1.185 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.541.70.56315730.5240.5630.7961.11888.3
2.54-2.591.80.49915450.5550.4990.7061.02987.7
2.59-2.641.80.46315920.5870.4630.6551.11487.4
2.64-2.691.80.44915860.6150.4490.6351.15889
2.69-2.751.80.34215110.7340.3420.4841.13585.4
2.75-2.821.70.30614640.7780.3060.4331.15682.6
2.82-2.891.70.31115510.7740.3110.441.26585.9
2.89-2.961.80.24116270.8630.2410.341.17791.4
2.96-3.051.80.20516290.8870.2050.291.19889.9
3.05-3.151.80.16915810.910.1690.2391.34489.1
3.15-3.261.80.13915830.9380.1390.1971.28988.2
3.26-3.391.80.11115060.9640.1110.1581.2685.4
3.39-3.551.70.114980.9690.10.1421.34682.4
3.55-3.731.80.08416040.9770.0840.1191.27691.5
3.73-3.971.80.06916360.980.0690.0981.19890.3
3.97-4.271.80.05515600.9880.0550.0781.11386.9
4.27-4.71.70.04814640.990.0480.0681.28882.3
4.7-5.381.80.03916260.9920.0390.0551.10991.1
5.38-6.781.80.03615440.9930.0360.0511.07486.7
6.78-501.80.02115980.9980.0210.0291.07289.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B3P

2b3p


Resolution: 2.483→34.742 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1580 5.06 %
Rwork0.1997 29673 -
obs0.202 31253 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.17 Å2 / Biso mean: 39.7837 Å2 / Biso min: 16.13 Å2
Refinement stepCycle: final / Resolution: 2.483→34.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 84 203 6401
Biso mean--40.45 39.07 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066328
X-RAY DIFFRACTIONf_angle_d0.8448578
X-RAY DIFFRACTIONf_chiral_restr0.055954
X-RAY DIFFRACTIONf_plane_restr0.0051078
X-RAY DIFFRACTIONf_dihedral_angle_d14.3463664
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3596X-RAY DIFFRACTION8.299TORSIONAL
12B3596X-RAY DIFFRACTION8.299TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.483-2.56290.35521060.2918233575
2.5629-2.65450.34631390.2728276988
2.6545-2.76070.32321540.2427268286
2.7607-2.88630.27571520.2414262084
2.8863-3.03840.27371500.2243288291
3.0384-3.22860.23061600.2075272989
3.2286-3.47770.23711490.192259083
3.4777-3.82730.22541380.1835287291
3.8273-4.38020.20771430.1796273388
4.3802-5.5150.26471510.1786270387
5.515-34.7420.18331380.1761275888
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.37520.6968-0.27662.8894-1.37512.7653-0.0723-0.07230.08720.1029-0.0717-0.1376-0.00540.09020.13070.15390.0386-0.04150.2003-0.0750.306533.3281-60.998951.3342
22.8976-0.8380.66613.30460.11011.9156-0.1059-0.0344-0.19050.31180.09270.16270.192-0.10870.01130.32170.0143-0.00940.2492-0.06830.237227.7828-15.006154.5223
31.79991.9172-1.32557.0851-3.45192.76530.1733-0.15720.32850.2034-0.21690.4159-0.2665-0.0994-0.01690.24970.0291-0.03370.3335-0.12130.353322.3823-56.878253.5687
46.7070.5783-1.79132.1093-0.76651.7821-0.0978-0.45860.88130.4450.1355-0.05920.05760.2713-0.0770.3229-0.0086-0.08480.2077-0.06250.432536.7227-55.204858.6589
52.1163-0.91210.62941.9016-0.142.8408-0.07480.19140.2251-0.1059-0.0403-0.2159-0.1170.21620.08710.1543-0.05840.02440.26510.03180.28834.209413.780320.1825
62.5547-0.39130.21638.181.79193.6647-0.19240.2628-0.5415-0.48540.3953-0.11410.0598-0.28-0.27320.24670.01430.01310.3767-0.04190.315229.2652-39.782922.0407
74.06191.21490.27172.65080.9893.9684-0.27410.25020.1095-0.81310.29370.2083-0.455-0.42010.01190.53440.0625-0.06770.3975-0.05050.296826.7889-27.301214.4293
84.3547-2.97234.02786.1679-5.01935.88480.2401-0.0101-0.04-0.2273-0.12370.3250.3642-0.1378-0.15080.2627-0.01980.05140.254-0.06630.287723.21679.828618.2196
95.2257-1.57472.33631.7798-1.61824.05920.05990.2376-0.381-0.0618-0.0351-0.18910.17310.43740.09450.25140.02740.00850.1955-0.01250.250337.51387.635912.8597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 151 )A2 - 151
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 296 )A152 - 296
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 350 )A297 - 350
4X-RAY DIFFRACTION4chain 'A' and (resid 351 through 384 )A351 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 151 )B2 - 151
6X-RAY DIFFRACTION6chain 'B' and (resid 152 through 206 )B152 - 206
7X-RAY DIFFRACTION7chain 'B' and (resid 207 through 296 )B207 - 296
8X-RAY DIFFRACTION8chain 'B' and (resid 297 through 350 )B297 - 350
9X-RAY DIFFRACTION9chain 'B' and (resid 351 through 384 )B351 - 384

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