SMTL ID : 9l54.1

cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with Vitamin K1 2,3-epoxide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.04 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: 4 residues within 4Å: Chain A: E.532, N.539, Y.559, T.561 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: T.496, N.519, V.573 No protein-ligand interaction detected (PLIP)

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

NAG.3: 7 residues within 4Å: Chain A: S.514, D.516, L.517, N.574, T.576, E.577 Chain B: L.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:E.577 Hydrogen bonds: A:D.516, B:L.13

1 x 01: (1~{a}~{R},7~{a}~{S})-7~{a}-methyl-1~{a}-[(~{E},7~{R},11~{R})-3,7,11,15-tetramethylhexadec-2-enyl]naphtho[2,3-b]oxirene-2,7-dione

01.4: 19 residues within 4Å: Chain A: Y.180, K.187, F.210, V.223, V.224, L.231, D.232, Y.254, F.255, H.256, M.258, N.259, L.262, F.263, I.265, F.268, M.272, M.371 Ligands: BCT.10 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.180, A:F.210, A:V.223, A:L.231, A:Y.254, A:F.255, A:M.258, A:L.262, A:F.263, A:F.268 Hydrogen bonds: A:K.187, A:N.259 pi-Stacking: A:F.255

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 9 residues within 4Å: Chain A: L.113, Y.117, Y.131, L.135, F.138, E.342, Q.343, L.346 Ligands: PEE.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.117, A:L.135, A:F.138, A:F.138 Hydrogen bonds: A:Y.131, A:Q.343

3 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.6: 15 residues within 4Å: Chain A: L.6, L.7, F.9, L.23, L.24, R.26, A.170, R.173, G.174, F.177, F.237, F.240, L.337, L.340, L.341 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.9, A:L.23, A:L.24, A:R.173, A:F.177, A:F.177, A:F.237, A:F.237, A:F.240, A:F.240, A:L.337, A:L.340, A:L.340, A:L.341 Hydrogen bonds: A:L.6, A:R.26 Salt bridges: A:R.173, A:R.173 PEE.7: 10 residues within 4Å: Chain A: F.42, L.46, Q.50, M.267, Y.270, F.653, K.657, L.658, F.661 Ligands: Y01.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.42, A:L.46, A:Y.270, A:L.658, A:F.661 Hydrogen bonds: A:Q.50, A:S.260 Salt bridges: A:K.657 PEE.9: 14 residues within 4Å: Chain A: P.71, L.72, L.73, D.74, W.116, L.120, L.346, Y.356, Y.366, D.411, Q.415, W.462, P.464 Ligands: CLR.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.116, A:L.120, A:L.346, A:Y.366 Hydrogen bonds: A:D.74, A:D.74

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 6 residues within 4Å: Chain A: M.99, F.661, R.662, F.665, L.666 Ligands: PEE.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.661, A:R.662, A:F.665, A:L.666

1 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.10: 7 residues within 4Å: Chain A: A.183, K.186, K.187, W.368, D.369, M.370 Ligands: 01.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.187, A:M.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, D. et al., cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with Vitamin K1 2,3-epoxide. To Be Published

Release Date

2025-10-22

Peptides

Vitamin K-dependent gamma-carboxylase: A
Vitamin K-dependent protein S: 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

Vitamin K-dependent protein S

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