6WVH: Human VKOR with Brodifacoum

Human VKOR with Brodifacoum. Determined by X-ray diffraction at 1.99 Å resolution. Released 11 Nov 2020.

Method: X-ray diffraction
Resolution: 1.99 Å
Organisms: Aequorea victoria, Homo sapiens
Chains: 2
Atoms: 6,682
Mol. weight: 90.15 kDa
Ligands: OLC, UA7
Released: 11 Nov 2020

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

Secondary structure: helices and β-sheets

6WVH contains 37 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: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
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	152-157	6
α-helix	161-177	17
β-strand	186-188	3	4
β-strand	191-192	2	4
α-helix	193-198	6
α-helix	200-202	3
β-strand	203	1	5
α-helix	204-206	3
α-helix	209-212	4
β-strand	221	1	5
α-helix	222-237	16
β-strand	239	1	3
α-helix	242-265	24
α-helix	266-270	5
α-helix	275-296	22
β-strand	302-307	6	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	348-349	2
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	4-8	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	79-81	3
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	186-187	2	9
β-strand	191-192	2	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	222-237	16
β-strand	239	1	8
α-helix	242-265	24
α-helix	266-270	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

>6WVH_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
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	2
UA7	Brodifacoum	C31 H23 Br 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:

6WV3 2.2 Å, Human VKOR with warfarin
6WV7 2.48 Å, Human VKOR with Chlorophacinone
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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