6WV7: Human VKOR with Chlorophacinone

Human VKOR with Chlorophacinone. Determined by X-ray diffraction at 2.48 Å resolution. Released 11 Nov 2020.

Method: X-ray diffraction
Resolution: 2.48 Å
Organisms: Aequorea victoria, Homo sapiens
Chains: 2
Atoms: 6,371
Mol. weight: 89.14 kDa
Ligands: UAJ
Released: 11 Nov 2020

Explore 6WV7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WV7 contains 35 α-helices and 40 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	11-22	12	1
β-strand	25-36	12	1
α-helix	37-39	3
β-strand	41-48	8	1
α-helix	57-60	4
α-helix	69-71	3
β-strand	73	1	1
α-helix	76-81	6
α-helix	83-86	4
β-strand	92-100	9	1
β-strand	105-115	11	1
β-strand	118-128	11	1
β-strand	141	1	2
β-strand	147	1	3
α-helix	152-176	25
β-strand	188	1	4
β-strand	191	1	4
α-helix	193-197	5
α-helix	200-202	3
β-strand	203	1	5
α-helix	204-206	3
α-helix	208-212	5
β-strand	221	1	5
α-helix	222-236	15
β-strand	239	1	3
α-helix	242-268	27
α-helix	275-297	23
β-strand	301-307	7	1
α-helix	308-310	3
β-strand	312-322	11	1
β-strand	323	1	2
β-strand	328-339	12	1
α-helix	346-349	4
β-strand	351-360	10	1
β-strand	369-379	11	1

Chain B: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	11-22	12	6
β-strand	25-36	12	6
α-helix	37-39	3
β-strand	41-48	8	6
α-helix	57-60	4
α-helix	69-71	3
β-strand	73	1	6
α-helix	76-81	6
α-helix	83-86	4
β-strand	92-100	9	6
β-strand	105-115	11	6
β-strand	118-128	11	6
β-strand	141	1	7
β-strand	147	1	8
α-helix	152-177	26
β-strand	188	1	9
β-strand	191	1	9
α-helix	193-198	6
α-helix	200-202	3
β-strand	203	1	10
α-helix	204-206	3
α-helix	208-210	3
α-helix	213-215	3
β-strand	221	1	10
α-helix	222-236	15
β-strand	239	1	8
α-helix	242-264	23
α-helix	265-269	5
α-helix	275-297	23
β-strand	302-307	6	6
α-helix	308-310	3
β-strand	312-322	11	6
β-strand	323	1	7
β-strand	328-339	12	6
α-helix	348-349	2
β-strand	351-360	10	6
β-strand	369-379	11	6
α-helix	386-388	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin K epoxide reductase, termini restrained by green fluorescent protein	A, B	protein	390	Aequorea victoria, Homo sapiens	Q9BQB6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6WV7_1 Vitamin K epoxide reductase, termini restrained by green fluorescent protein (chains A, B)
MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTL
VTTLXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNR
IELKGIDFKEDGNILGHKLEYNSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYR
ALCDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTR
WASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQENSHNV
YITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKD
PNEKRDHMVLLEFVTAAGITHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
UAJ	Chlorophacinone	C23 H15 Cl O3	2

Primary citation

Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation. Liu, S., Li, S., Shen, G. et al. Science (2021) 371. DOI 10.1126/science.abc5667 · PubMed

Other PDB entries of the same protein (UniProt Q9BQB6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WVH 1.99 Å, Human VKOR with Brodifacoum
6WV3 2.2 Å, Human VKOR with warfarin
6WV6 2.7 Å, Human VKOR with phenindione
6WV5 2.8 Å, Human VKOR C43S mutant with vitamin K1 epoxide
6WV4 3.01 Å, Human VKOR C43S with warfarin

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