SMTL ID : 8urp.1

Cholinephosphotransferase in complex with CDP-choline and phosphatidylcholine

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: D.96, D.99, D.117 Ligands: MG.2, CDC.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.96, A:D.96, A:D.99, A:D.117 MG.2: 5 residues within 4Å: Chain A: D.96, D.117, D.121 Ligands: MG.1, CDC.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.96, A:D.96, A:D.117, A:D.121, A:D.121 MG.10: 5 residues within 4Å: Chain B: D.96, D.99, D.117 Ligands: MG.11, CDC.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.96, B:D.96, B:D.99, B:D.99, B:D.117 MG.11: 5 residues within 4Å: Chain B: D.96, D.117, D.121 Ligands: MG.10, CDC.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.96, B:D.96, B:D.117, B:D.121, B:D.121

6 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.3: 13 residues within 4Å: Chain A: F.3, R.307, V.321, N.322, F.323, M.356 Chain B: L.362, A.363, M.367, N.370, Y.374 Ligands: PCW.4, PCW.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.323, A:F.323 Hydrogen bonds: A:V.321, A:F.323 Salt bridges: A:R.307, A:R.307 pi-Cation interactions: A:F.3 PCW.4: 18 residues within 4Å: Chain A: V.333, F.337, M.338, D.343, Y.344, Q.345, S.348, I.349, A.352, M.356 Chain B: V.63, L.67, P.71, Y.72, L.291, W.355 Ligands: PCW.3, PCW.9 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.63, B:L.67, B:P.71, B:L.291, B:W.355, A:V.333, A:F.337, A:F.337, A:I.349 Hydrogen bonds: A:S.348 PCW.7: 17 residues within 4Å: Chain A: P.71, Y.72, L.291, W.355, L.362 Chain B: L.334, F.337, M.338, D.343, Y.344, Q.345, S.348, I.349, A.352, M.356 Ligands: PCW.8, PCW.12 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.334, B:F.337, B:F.337, B:I.349, A:P.71, A:W.355, A:W.355 Hydrogen bonds: B:Q.345, B:S.348, B:S.348, A:Y.72 pi-Cation interactions: B:Y.344 PCW.8: 18 residues within 4Å: Chain A: L.53, F.56, I.60, L.115, F.116, C.119, I.120, I.123, L.127, H.365, G.366, I.369, N.370, I.373, Y.383, A.384, L.385 Ligands: PCW.7 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.53, A:F.56, A:L.115, A:F.116, A:F.116, A:F.116, A:F.116, A:I.120, A:I.123, A:L.127, A:L.127, A:I.369, A:I.373, A:I.373 Hydrogen bonds: A:N.370, A:A.384, A:L.385 pi-Cation interactions: A:Y.383 PCW.9: 19 residues within 4Å: Chain B: L.53, F.56, L.115, F.116, C.119, I.120, I.123, L.127, F.299, H.365, G.366, I.369, N.370, I.373, Y.383, A.384, L.385 Ligands: PCW.3, PCW.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.53, B:F.56, B:L.115, B:F.116, B:F.116, B:F.116, B:I.120, B:I.123, B:L.127, B:L.127, B:F.299, B:I.369, B:I.369, B:I.373, B:L.385 Hydrogen bonds: B:A.384 pi-Cation interactions: B:Y.383 PCW.12: 13 residues within 4Å: Chain A: G.366, M.367, Y.374 Chain B: F.3, F.4, R.307, V.321, F.323, I.330, L.334, L.360, I.364 Ligands: PCW.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.323, B:F.323, B:I.330, B:L.334, B:L.360, B:I.364 Salt bridges: B:R.307, B:R.307 pi-Cation interactions: B:F.3

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

CDC.5: 22 residues within 4Å: Chain A: Y.16, Y.18, S.27, W.35, P.48, N.49, T.52, D.96, A.97, D.99, G.100, A.103, R.104, Q.108, Q.109, G.110, G.113, E.114, D.117, L.168 Ligands: MG.1, MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.117 Hydrogen bonds: A:Y.16, A:Y.18, A:Y.18, A:T.52, A:T.52, A:G.100, A:R.104, A:G.110, A:E.114, A:E.114 Salt bridges: A:D.22, A:R.104 CDC.13: 24 residues within 4Å: Chain B: Y.16, Y.18, S.27, W.35, P.48, N.49, T.52, D.96, A.97, D.99, G.100, A.103, R.104, Q.108, Q.109, G.110, G.113, E.114, D.117, L.168, L.170, V.177 Ligands: MG.10, MG.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:D.117 Hydrogen bonds: B:Y.16, B:T.52, B:T.52, B:A.97, B:G.100, B:R.104, B:G.110, B:E.114 Salt bridges: B:D.22, B:R.104

2 x PCF: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE(Non-covalent)

PCF.6: 22 residues within 4Å: Chain A: D.96, E.114, H.118, D.121, N.124, T.125, S.128, S.147, I.151, S.154, F.155, S.158, T.159, E.162, L.168, G.175, P.176, G.179, V.182, L.183, M.221, C.225 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.182, A:L.183 Hydrogen bonds: A:D.96, A:S.158 Salt bridges: A:H.118, A:E.162 pi-Cation interactions: A:H.118 PCF.14: 23 residues within 4Å: Chain B: Y.92, H.118, D.121, N.124, T.125, S.128, M.129, I.151, S.154, F.155, S.158, T.159, E.162, L.168, G.175, P.176, G.179, V.182, L.183, M.221, Y.222, F.224, C.225 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.92, B:N.124, B:L.183, B:L.183, B:F.224 Hydrogen bonds: B:Y.92 Salt bridges: B:E.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roberts, J.R. et al., Structural basis for catalysis and selectivity of phospholipid synthesis by eukaryotic choline-phosphotransferase. Nat Commun (2025)

Release Date

2024-10-30

Peptides

Cholinephosphotransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Cholinephosphotransferase 1

Related Entries With Identical Sequence