SMTL ID : 9l20.1

cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with anisindione

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.82 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: T.530, Q.537, 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: 6 residues within 4Å: Chain A: S.514, D.516, L.517, N.574, T.576, E.577 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.577 Hydrogen bonds: A:D.516

1 x 01: 2-(4-methoxyphenyl)-1H-indene-1,3(2H)-dione

01.4: 14 residues within 4Å: Chain A: Y.180, K.187, W.192, L.201, D.232, F.255, H.256, N.259, F.263, F.268, M.272, M.370, M.371 Ligands: BCT.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.180, A:F.255, A:F.268 Hydrogen bonds: A:K.187, A:N.259 pi-Cation interactions: A:K.187

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 8 residues within 4Å: Chain A: L.113, W.116, Y.117, Y.131, F.138, E.342, Q.343, L.346 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.113, A:W.116, A:W.116, A:W.116, 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: 13 residues within 4Å: Chain A: L.6, L.7, F.9, R.26, L.166, A.170, R.173, G.174, F.240, D.242, L.337, L.340, L.341 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.7, A:F.9, A:R.173, A:F.240, A:F.240, A:L.340, A:L.340, A:L.341 Hydrogen bonds: A:R.26, A:D.242 Salt bridges: A:R.173, A:R.173 PEE.7: 12 residues within 4Å: Chain A: V.35, L.39, Q.50, M.267, Y.270, A.274, P.277, W.284, F.653, K.657, F.661 Ligands: Y01.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.35, A:L.39, A:Y.270, A:Y.270, A:A.274, A:F.653, A:K.657, A:F.661 Salt bridges: A:K.657 PEE.9: 11 residues within 4Å: Chain A: L.72, D.74, L.120, Y.356, Y.366, D.411, K.414, Q.415, W.462, P.464, F.465 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.120, A:Y.366, A:Y.366, A:F.465 Hydrogen bonds: A:P.71 Salt bridges: A:K.123

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 8 residues within 4Å: Chain A: F.42, V.45, M.99, F.661, R.662, F.665, Y.691 Ligands: PEE.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.661, A:R.662, A:F.665

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 anisindione. 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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