SMTL ID : 9bvr.1

Vitamin K-dependent gamma-carboxylase with factor IX propeptide and partially carboxylated glutamate-rich region and with vitamin K hydroquinone and calcium

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: 5 residues within 4Å: Chain A: G.511, T.535, E.537, Q.542, N.544 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: T.501, N.524, S.526, V.576, V.578 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.519, D.521, L.522, N.579, E.582 No protein-ligand interaction detected (PLIP)

1 x 01: vitamin K1 hydroquinone

01.4: 18 residues within 4Å: Chain A: Y.185, K.192, W.197, M.203, F.212, V.228, V.229, D.237, Y.259, F.260, H.261, M.263, N.264, F.268, I.270, F.273, M.375, M.376 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.185, A:W.197, A:F.212, A:Y.259, A:F.260, A:F.268, A:F.273, A:M.376 Hydrogen bonds: A:K.192, A:N.264 pi-Stacking: A:F.260

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.5: 16 residues within 4Å: Chain A: L.11, L.12, G.13, F.14, L.19, L.29, R.31, L.171, A.175, R.178, F.182, F.242, F.245, F.246, D.247, R.250 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.29, A:F.182, A:F.182, A:F.242, A:F.245, A:F.246 Salt bridges: A:R.31, A:R.178, A:R.178, A:D.247 pi-Cation interactions: A:F.245 6PL.6: 10 residues within 4Å: Chain A: L.48, Q.55, S.265, F.268, S.269, M.272, Y.275, F.656, F.658, K.662 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.48, A:F.656 Hydrogen bonds: A:Q.55 Salt bridges: A:K.662, A:K.662

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

NAG.7: 1 residues within 4Å: Chain A: N.433 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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
Coagulation factor IX: 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

Coagulation factor IX

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