SMTL ID : 9mqb.1

Vitamin K-dependent gamma-carboxylase with Osteocalcin (mutant) and vitamin K hydroquinone and calcium

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 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: 7 residues within 4Å: Chain A: G.537, T.561, E.563, Q.568, N.570, Y.590, T.592 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: T.527, N.550, S.552, K.578, V.602, V.604 No protein-ligand interaction detected (PLIP)

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

NAG.3: 10 residues within 4Å: Chain A: S.545, D.547, L.548, N.605, T.607, E.608 Chain B: L.46, K.47, R.48 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.548 Hydrogen bonds: A:D.547, A:E.608 NAG.4: 2 residues within 4Å: Chain A: L.611 Ligands: NAG.3 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: N.459 Chain B: K.32 No protein-ligand interaction detected (PLIP)

2 x 6PL: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

6PL.6: 24 residues within 4Å: Chain A: K.36, L.37, L.38, G.39, F.40, L.45, W.48, L.51, L.54, L.55, R.57, L.197, A.201, R.204, G.205, F.208, G.267, F.268, F.271, F.272, D.273, R.276, F.310, L.368 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.55, A:F.208, A:F.208, A:F.268, A:F.271 Salt bridges: A:R.204, A:R.204, A:D.273 pi-Cation interactions: A:F.271 6PL.7: 24 residues within 4Å: Chain A: L.70, F.73, L.74, L.77, Q.81, S.291, Q.292, F.294, S.295, G.297, M.298, Y.301, L.304, A.305, P.308, W.315, F.682, F.684, L.685, L.686, K.688, L.689, F.692 Chain B: R.70 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Salt bridges: B:R.70, A:K.688, A:K.688 Hydrophobic interactions: A:L.74, A:W.315, A:F.682, A:L.685, A:F.692

1 x 01: vitamin K1 hydroquinone

01.8: 28 residues within 4Å: Chain A: V.210, Y.211, A.214, K.218, W.223, M.229, L.232, F.238, F.241, V.254, V.255, G.258, G.259, L.261, L.262, D.263, Y.285, F.286, H.287, M.289, N.290, L.293, F.294, I.296, F.299, M.303, M.401, M.402 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.211, A:F.238, A:L.262, A:F.286, A:F.294, A:F.299 Hydrogen bonds: A:K.218, A:N.290 pi-Stacking: A:F.286, A:F.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Q. et al., Structural insights into the vitamin K-dependent gamma-carboxylation of osteocalcin. Cell Res. (2025)

Release Date

2025-10-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
P

Membrane

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

Osteocalcin

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