SMTL ID : 9l6s.1

double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with coagulation factors X and vitamin K

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.58 Å

Oligo State

hetero-1-1-mer

Ligands

2 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.1: 5 residues within 4Å: Chain B: L.523, D.524, T.527, N.550, V.604 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.523 NAG-NAG-BMA.3: 8 residues within 4Å: Chain A: L.35, R.37 Chain B: S.545, D.547, L.548, N.605, T.607, E.608 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain B: E.563, N.570, Y.590 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.590

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

NAG.4: 2 residues within 4Å: Chain B: R.419, N.459 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.459

1 x 01: 2-methyl-3-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]naphthalene-1,4-diol

01.5: 24 residues within 4Å: Chain B: Y.211, W.223, M.229, L.232, F.238, F.241, V.254, V.255, G.258, G.259, L.262, D.263, F.282, Y.285, F.286, H.287, M.289, N.290, F.294, I.296, F.299, M.303, M.401, M.402 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.223, B:V.255, B:L.262, B:F.282, B:F.286, B:F.286, B:F.294, B:F.299, B:F.299 Hydrogen bonds: B:D.263, B:N.290 pi-Stacking: B:F.286

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.6: 14 residues within 4Å: Chain B: L.37, L.38, G.39, F.40, L.45, L.54, L.55, R.57, L.197, A.201, R.204, F.208, F.271, R.276 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.40, B:L.45, B:L.54, B:L.55, B:R.204, B:F.208, B:F.271, B:F.271, B:F.271, B:F.271 Hydrogen bonds: B:R.57 Salt bridges: B:R.204, B:R.204 pi-Cation interactions: B:F.271 6PL.7: 14 residues within 4Å: Chain B: L.70, L.77, Q.81, S.291, Q.292, F.294, S.295, M.298, Y.301, L.304, W.315, F.684, K.688, L.689 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.70, B:L.77, B:Y.301, B:W.315, B:K.688, B:L.689 Hydrogen bonds: B:Q.81 Salt bridges: B:K.688, B:K.688

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.8: 7 residues within 4Å: Chain B: W.147, Y.162, L.166, F.169, E.373, Q.374, L.377 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.147, B:W.147, B:L.166, B:F.169 Hydrogen bonds: B:Y.162, B:Y.162, B:Q.374

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

Membrane

We predict this structure to be a membrane protein.
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Coagulation factor X

Vitamin K-dependent gamma-carboxylase

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