SMTL ID : 9bur.1

Structure of GGCX-BGP 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: 4 residues within 4Å: Chain A: 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: 2 residues within 4Å: Chain A: T.527, N.550 No protein-ligand interaction detected (PLIP) NAG.3: 9 residues within 4Å: Chain A: S.545, D.547, L.548, N.605, T.607, E.608, L.611 Chain B: V.46, K.47 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.548, B:V.46 Hydrogen bonds: A:D.547, A:D.547, A:E.608

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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.144, A:W.147, A:W.147, A:F.169, 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: 17 residues within 4Å: Chain A: L.37, L.38, G.39, F.40, L.54, L.55, R.57, L.197, R.204, G.205, F.208, F.268, F.271, D.273, R.276, L.368, L.371 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.40, A:L.54, A:R.204, A:F.208, A:F.268, A:F.271, A:L.368, A:L.371 Salt bridges: A:R.57, A:R.204, A:R.204, A:D.273 pi-Cation interactions: A:F.271

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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