SMTL ID : 9bux.1

Structure of GGCX-BGP-menaquinone-4 epoxide complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: T.561, E.563, Q.568, N.570, Y.590 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.550 No protein-ligand interaction detected (PLIP) NAG.3: 7 residues within 4Å: Chain A: D.547, L.548, N.605, T.607, E.608, L.611 Chain B: K.47 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.548 Hydrogen bonds: A:D.547, A:D.547, A:N.605

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 8 residues within 4Å: Chain A: L.144, W.147, Y.162, L.166, F.169, E.373, Q.374, L.377 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.144, A:W.147, A:W.147, A:W.147, A:L.166, A:F.169, A:L.377 Hydrogen bonds: A:Y.162, A:Q.374

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.5: 19 residues within 4Å: Chain A: I.34, K.36, L.37, L.38, G.39, F.40, L.54, L.55, R.57, L.197, R.204, F.208, F.268, F.271, D.273, R.276, T.367, L.371, L.372 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.34, A:L.38, A:F.40, A:R.204, A:F.208, A:F.208, A:F.268, A:F.271, A:F.271, A:T.367, A:L.372 Hydrogen bonds: A:G.39, A:R.57 Salt bridges: A:R.204, A:R.204, A:D.273 pi-Cation interactions: A:F.271

1 x 01: (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione

01.6: 18 residues within 4Å: Chain A: V.210, Y.211, A.214, K.218, W.223, F.241, L.253, V.254, G.258, L.262, D.263, F.282, F.286, H.287, M.289, N.290, F.299, M.401 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.210, A:Y.211, A:Y.211, A:A.214, A:W.223, A:W.223, A:F.241, A:L.262, A:F.282, A:F.286, A:F.286, A:M.289, A:N.290, A:F.299, A:F.299 Hydrogen bonds: A:K.218, A:N.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, R. et al., Structure and mechanism of vitamin-K-dependent gamma-glutamyl carboxylase. Nature (2025)

Release Date

2025-01-29

Peptides

Vitamin K-dependent gamma-carboxylase: A
Osteocalcin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Vitamin K-dependent gamma-carboxylase

Osteocalcin

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