SMTL ID : 8erp.1

Structure of Xenopus cholinephosphotransferase1 in complex with CDP-choline

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: Y.107, D.111, D.132, D.136 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.111, A:D.132, A:D.136, A:D.136 MG.2: 5 residues within 4Å: Chain A: D.111, D.114, D.132 Ligands: MG.1, CDC.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.111, A:D.132 MG.16: 5 residues within 4Å: Chain B: Y.107, D.111, D.132, D.136 Ligands: MG.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.111, B:D.132, B:D.136, B:D.136 MG.17: 5 residues within 4Å: Chain B: D.111, D.114, D.132 Ligands: MG.16, CDC.20 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.111, B:D.132

20 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)(Non-functional Binders)

LBN.3: 2 residues within 4Å: Chain A: I.353 Ligands: LBN.4 No protein-ligand interaction detected (PLIP) LBN.4: 1 residues within 4Å: Ligands: LBN.3 No protein-ligand interaction detected (PLIP) LBN.6: 9 residues within 4Å: Chain A: L.273, Q.325, D.326, I.330, G.333, F.337, F.344, I.345 Ligands: LBN.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.273, A:F.337, A:F.344, A:I.345 Hydrogen bonds: A:Q.325 LBN.7: 5 residues within 4Å: Chain A: L.79, V.82, L.296, L.299, M.355 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.79, A:V.82, A:L.296, A:L.299 LBN.8: 1 residues within 4Å: Chain A: K.283 No protein-ligand interaction detected (PLIP) LBN.9: 3 residues within 4Å: Chain A: L.276, K.283 Ligands: LBN.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.276, A:K.283 LBN.10: 4 residues within 4Å: Chain A: M.68, C.366, V.381, F.382 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.381, A:F.382 LBN.11: 3 residues within 4Å: Chain A: L.79, I.80, Y.84 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.79, A:I.80 LBN.12: 2 residues within 4Å: Chain A: F.337 Ligands: LBN.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.337 LBN.13: 3 residues within 4Å: Chain A: F.341, S.343 Ligands: LBN.24 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.341 LBN.14: 2 residues within 4Å: Chain B: F.337 Ligands: LBN.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.337 LBN.15: 3 residues within 4Å: Chain B: F.341, S.343 Ligands: LBN.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.341 LBN.18: 2 residues within 4Å: Chain B: I.353 Ligands: LBN.19 No protein-ligand interaction detected (PLIP) LBN.19: 1 residues within 4Å: Ligands: LBN.18 No protein-ligand interaction detected (PLIP) LBN.21: 9 residues within 4Å: Chain B: L.273, Q.325, D.326, I.330, G.333, F.337, F.344, I.345 Ligands: LBN.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.273, B:F.337, B:F.344, B:I.345 Hydrogen bonds: B:Q.325 LBN.22: 5 residues within 4Å: Chain B: L.79, V.82, L.296, L.299, M.355 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.79, B:V.82, B:L.296, B:L.299 LBN.23: 1 residues within 4Å: Chain B: K.283 No protein-ligand interaction detected (PLIP) LBN.24: 3 residues within 4Å: Chain B: L.276, K.283 Ligands: LBN.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.276, B:K.283 LBN.25: 4 residues within 4Å: Chain B: M.68, C.366, V.381, F.382 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.381, B:F.382 LBN.26: 3 residues within 4Å: Chain B: L.79, I.80, Y.84 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.79, B:I.80

2 x CDC: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM(Non-covalent)

CDC.5: 15 residues within 4Å: Chain A: Y.34, W.50, P.63, N.64, T.67, D.111, G.115, A.118, R.119, G.128, E.129, D.132, F.186, T.192 Ligands: MG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.34, A:Y.34, A:N.64, A:S.125 Salt bridges: A:E.43, A:R.119 CDC.20: 15 residues within 4Å: Chain B: Y.34, W.50, P.63, N.64, T.67, D.111, G.115, A.118, R.119, G.128, E.129, D.132, F.186, T.192 Ligands: MG.17 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.34, B:Y.34, B:N.64, B:S.125 Salt bridges: B:E.43, B:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Structure of a eukaryotic cholinephosphotransferase-1 reveals mechanisms of substrate recognition and catalysis. Nat Commun (2023)

Release Date

2023-04-26

Peptides

Cholinephosphotransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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Cholinephosphotransferase 1

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