SMTL ID : 9bvq.1

Vitamin K-dependent gamma-carboxylase with TMG2 propeptide and glutamate-rich region

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

3 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: T.535, E.537, Q.542, N.544 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: T.501, N.524, V.576 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 9 residues within 4Å: Chain A: S.519, D.521, L.522, N.579, E.582, L.585 Chain B: H.21, T.22, R.23 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.4: 13 residues within 4Å: Chain A: L.11, L.12, G.13, F.14, L.171, A.175, R.178, G.179, F.182, F.242, F.245, D.247, R.250 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.182, A:F.242, A:F.245 Salt bridges: A:R.178, A:R.178, A:D.247 pi-Cation interactions: A:F.245 6PL.5: 14 residues within 4Å: Chain A: F.47, L.48, Q.55, S.265, Q.266, F.268, S.269, M.272, Y.275, F.656, F.658, L.659, K.662, F.666 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.47, A:L.48, A:F.656, A:L.659, A:K.662, A:F.666 Salt bridges: A:K.662, A:K.662

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

NAG.6: 2 residues within 4Å: Chain A: N.433 Chain B: D.4 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.4, A:N.433, A:N.433

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Q. et al., Structural basis of vitamin K dependent gamma-carboxylation. To Be Published

Release Date

2025-01-22

Peptides

Vitamin K-dependent gamma-carboxylase: A
Transmembrane gamma-carboxyglutamic acid protein 2: 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

Transmembrane gamma-carboxyglutamic acid protein 2

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