SMTL ID : 9l6q.1

Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.78 Å

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: 5 residues within 4Å: Chain A: L.523, D.524, T.527, N.550, V.604 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.524 NAG-NAG.2: 7 residues within 4Å: Chain A: G.537, T.561, E.563, Q.568, N.570, Y.590, T.592 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.590

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 9 residues within 4Å: Chain A: S.545, D.547, L.548, N.605, T.607, E.608, L.611 Chain B: N.42, R.43 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: 22 residues within 4Å: Chain A: L.70, F.73, L.74, L.77, Q.81, S.291, F.294, S.295, 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, F.728 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.70, A:F.73, A:Y.301, A:L.304, A:P.308, A:W.315, A:F.682, A:L.685, A:L.686, A:F.692, A:F.692 Hydrogen bonds: A:Q.81 Salt bridges: A:K.688, A:K.688 6PL.5: 19 residues within 4Å: Chain A: L.37, L.38, G.39, F.40, L.45, S.46, S.47, L.51, L.55, R.57, L.197, A.201, R.204, G.205, F.208, F.268, F.271, D.273, R.276 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.38, A:L.51, A:R.204, A:F.208, A:F.208, A:F.268, A:F.271, A:F.271, A:F.271, A:F.271 Salt bridges: A:R.57, A:R.204, A:D.273 pi-Cation interactions: A:F.271

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 10 residues within 4Å: Chain A: L.107, L.144, W.147, Y.148, Y.162, L.166, F.169, E.373, Q.374, L.377 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.107, A:L.144, A:W.147, A:W.147, A:W.147, A:Y.148, A:F.169, A:L.377 Hydrogen bonds: A:Y.162, A:Y.162, A:Q.374

1 x 1L3: Menaquinone-4(Non-covalent)

1L3.7: 23 residues within 4Å: Chain A: V.210, A.214, K.218, W.223, L.232, F.238, F.241, L.253, V.254, V.255, W.257, G.258, G.259, D.263, Y.285, F.286, N.290, F.294, I.296, F.299, M.303, M.401, M.402 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.223, A:L.232, A:F.238, A:F.241, A:V.254, A:V.255, A:Y.285, A:F.286, A:F.286, A:F.286, A:F.294, A:F.294, A:F.299 Hydrogen bonds: A:N.290 pi-Stacking: A:F.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hang, J. et al., double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX peptide and vitamin K. To Be Published

Release Date

2025-10-08

Peptides

Vitamin K-dependent gamma-carboxylase: A
Coagulation factor IX: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

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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