SMTL ID : 9l25.1

cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX(Gla)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.41 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: E.532, Q.537, N.539, Y.559, T.561 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: 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: D.516, L.517, N.574, E.577 Chain B: L.13, N.14, R.15 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:L.13, B:R.15, A:E.577, A:E.577 Hydrophobic interactions: A:E.577

1 x 01: vitamin K1 hydroquinone

01.4: 24 residues within 4Å: Chain A: V.179, Y.180, A.183, K.187, W.192, F.207, F.210, V.223, V.224, G.227, D.232, F.250, F.251, Y.254, F.255, H.256, N.259, L.262, F.263, F.268, M.272, M.370, M.371 Ligands: BCT.11 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.179, A:Y.180, A:Y.180, A:A.183, A:W.192, A:F.207, A:F.210, A:F.250, A:F.251, A:Y.254, A:F.255, A:F.255, A:F.255, A:L.262, A:F.263, 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, W.116, Y.131, L.135, F.138, E.342, Q.343, L.346 Ligands: PEE.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.113, A:W.116, A:W.116, A:L.135, A:F.138, A:F.138, A:L.346 Hydrogen bonds: A:Y.131, A:Q.343

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

PEE.6: 18 residues within 4Å: Chain A: L.6, L.7, G.8, F.9, L.23, L.24, R.26, L.166, A.170, R.173, G.174, F.177, F.237, F.240, D.242, L.337, L.340, L.341 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.7, A:F.9, A:F.9, A:L.23, A:L.24, A:R.173, A:F.177, A:F.177, A:F.177, A:F.237, A:F.240, 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: 19 residues within 4Å: Chain A: V.35, F.36, L.39, F.42, L.43, L.46, Q.50, S.264, M.267, Y.270, L.273, A.274, P.277, W.284, F.653, K.657, L.658, F.661 Ligands: Y01.8 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.39, A:F.42, A:L.46, A:Y.270, A:Y.270, A:P.277, A:P.277, A:W.284, A:W.284, A:K.657, A:L.658, A:L.658, A:F.661 Hydrogen bonds: A:Q.50, A:S.264, A:S.264 Salt bridges: A:K.657 PEE.9: 18 residues within 4Å: Chain A: P.71, L.72, L.73, D.74, L.120, L.346, T.353, Y.356, L.363, Y.366, D.411, K.414, Q.415, T.418, W.462, P.464, F.465 Ligands: CLR.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.72, A:L.72, A:L.120, A:L.346, A:T.353, A:Y.356, A:L.363, A:Y.366, A:Y.366, A:Y.366, A:F.465 Hydrogen bonds: A:L.72, A:K.414 Water bridges: A:Y.356, A:Y.356, A:C.419 Salt bridges: A:K.123

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 7 residues within 4Å: Chain A: F.42, V.45, 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 CO2: CARBON DIOXIDE(Non-covalent)

CO2.10: 5 residues within 4Å: Chain A: N.128, H.129, F.268, M.370 Chain B: E.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.26

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

BCT.11: 8 residues within 4Å: Chain A: A.183, K.186, K.187, D.232, W.368, D.369, M.370 Ligands: 01.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.183, 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 factor IX(Gla). To Be Published

Release Date

2025-10-22

Peptides

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

Coagulation factor IX

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