SMTL ID : 9l21.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.62 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, Q.537, N.539, Y.559 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: T.496, N.519 No protein-ligand interaction detected (PLIP)

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

NAG.3: 8 residues within 4Å: Chain A: D.516, L.517, N.574, T.576, E.577 Chain B: L.13, N.14, R.15 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.13, B:R.15, A:D.516 Hydrophobic interactions: A:E.577

1 x 01: vitamin K1 hydroquinone

01.4: 15 residues within 4Å: Chain A: Y.180, A.183, K.187, F.210, V.223, V.224, D.232, Y.254, F.255, H.256, N.259, F.263, F.268, M.371 Ligands: BCT.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.180, A:Y.180, A:A.183, A:F.255, A:F.263, A:F.263, A:F.268 Hydrogen bonds: A:K.187, A:K.187 pi-Stacking: A:F.255, A:F.255

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

BCT.5: 7 residues within 4Å: Chain A: A.183, K.186, K.187, 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

1 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.6: 5 residues within 4Å: Chain A: N.128, H.129, F.268, M.370 Chain B: E.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.25

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 10 residues within 4Å: Chain A: L.113, W.116, Y.117, Y.131, L.135, F.138, E.342, Q.343, L.346 Ligands: PEE.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.116, A:W.116, A:Y.117, A:L.135, A:F.138 Hydrogen bonds: A:Y.131, A:Q.343

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

PEE.8: 14 residues within 4Å: Chain A: L.6, L.7, G.8, F.9, L.23, R.26, A.170, R.173, G.174, F.177, G.236, F.240, L.340, L.341 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.7, A:F.9, A:F.9, A:L.23, A:R.173, A:F.177, A:F.177, A:F.240, A:F.240, A:F.240, A:L.340, A:L.341 Hydrogen bonds: A:R.26, A:F.240 Salt bridges: A:R.173, A:R.173 PEE.9: 16 residues within 4Å: Chain A: S.32, V.35, F.36, L.39, L.43, L.46, Q.50, M.267, Y.270, L.273, A.274, P.277, W.284, F.653, K.657 Ligands: Y01.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.35, A:L.39, A:L.43, A:Y.270, A:Y.270, A:P.277, A:P.277, A:K.657 Hydrogen bonds: A:Q.50 Salt bridges: A:K.657 PEE.11: 14 residues within 4Å: Chain A: P.71, L.72, L.73, D.74, L.120, Y.356, Y.366, D.411, K.414, Q.415, T.418, W.462, P.464 Ligands: CLR.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.72, A:L.120, A:Y.366, A:Y.366 Hydrogen bonds: A:L.72, A:K.414 Water bridges: A:K.123, A:Y.356 Salt bridges: A:K.123

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.10: 7 residues within 4Å: Chain A: F.42, V.45, F.661, R.662, F.665, Y.691 Ligands: PEE.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.661, A:R.662, A:F.665

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. 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.
Show / Hide

Vitamin K-dependent gamma-carboxylase

Coagulation factor IX

Related Entries With Identical Sequence