SMTL ID : 8ero.1

Structure of Xenopus cholinephosphotransferase1 in complex with CDP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: Y.107, D.111, D.132, D.136 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.111, A:D.132, A:D.136 MG.2: 4 residues within 4Å: Chain A: D.111, D.114, D.132 Ligands: CDP.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.111, A:D.132 MG.20: 4 residues within 4Å: Chain B: Y.107, D.111, D.132, D.136 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.111, B:D.132, B:D.136 MG.21: 4 residues within 4Å: Chain B: D.111, D.114, D.132 Ligands: CDP.32 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.111, B:D.132

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

LBN.3: 2 residues within 4Å: Chain A: T.327, A.360 No protein-ligand interaction detected (PLIP) LBN.4: 12 residues within 4Å: Chain A: Q.325, D.326, T.327, I.330, G.333, F.337, F.344, I.345 Chain B: F.337 Ligands: LBN.14, LBN.16, LBN.17 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.337, A:F.337, A:F.344, A:I.345, B:F.337 Hydrogen bonds: A:Q.325 LBN.5: 3 residues within 4Å: Chain A: L.79, L.299, M.355 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.79, A:L.79, A:L.299 LBN.6: 2 residues within 4Å: Chain A: L.279, K.283 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.279 LBN.7: 4 residues within 4Å: Chain A: L.276, K.283, K.284 Ligands: LBN.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.276, A:K.283 LBN.8: 3 residues within 4Å: Chain A: C.366, C.370, V.381 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.381 LBN.9: 4 residues within 4Å: Chain A: L.79, I.80, C.83, Y.84 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.80, A:Y.84 LBN.10: 1 residues within 4Å: Chain A: L.269 No protein-ligand interaction detected (PLIP) LBN.11: 2 residues within 4Å: Chain A: L.156, W.159 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.159 LBN.12: 4 residues within 4Å: Chain A: W.352, I.353, V.356, F.359 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.352, A:I.353, A:V.356, A:V.356, A:F.359 Hydrogen bonds: A:Y.348 LBN.14: 2 residues within 4Å: Ligands: LBN.4, LBN.23 No protein-ligand interaction detected (PLIP) LBN.15: 4 residues within 4Å: Chain A: F.341, N.342, S.343 Ligands: LBN.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.341, A:F.341, A:N.342 LBN.16: 3 residues within 4Å: Chain A: Q.325 Chain B: L.269 Ligands: LBN.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.269 LBN.17: 2 residues within 4Å: Ligands: LBN.4, LBN.23 No protein-ligand interaction detected (PLIP) LBN.18: 4 residues within 4Å: Chain B: F.341, N.342, S.343 Ligands: LBN.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.341, B:F.341, B:N.342 LBN.19: 3 residues within 4Å: Chain A: L.269 Chain B: Q.325 Ligands: LBN.23 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.269 LBN.22: 2 residues within 4Å: Chain B: T.327, A.360 No protein-ligand interaction detected (PLIP) LBN.23: 12 residues within 4Å: Chain A: F.337 Chain B: Q.325, D.326, T.327, I.330, G.333, F.337, F.344, I.345 Ligands: LBN.14, LBN.17, LBN.19 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.337, B:F.337, B:F.344, B:I.345, A:F.337 Hydrogen bonds: B:Q.325 LBN.24: 3 residues within 4Å: Chain B: L.79, L.299, M.355 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.79, B:L.79, B:L.299 LBN.25: 2 residues within 4Å: Chain B: L.279, K.283 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.279 LBN.26: 4 residues within 4Å: Chain B: L.276, K.283, K.284 Ligands: LBN.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.276, B:K.283 LBN.27: 3 residues within 4Å: Chain B: C.366, C.370, V.381 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.381 LBN.28: 4 residues within 4Å: Chain B: L.79, I.80, C.83, Y.84 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.80, B:Y.84 LBN.29: 1 residues within 4Å: Chain B: L.269 No protein-ligand interaction detected (PLIP) LBN.30: 2 residues within 4Å: Chain B: L.156, W.159 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.159 LBN.31: 4 residues within 4Å: Chain B: W.352, I.353, V.356, F.359 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.352, B:I.353, B:V.356, B:V.356, B:F.359 Hydrogen bonds: B:Y.348

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.13: 12 residues within 4Å: Chain A: Y.34, P.63, N.64, D.111, G.115, A.118, R.119, S.124, S.125, G.128, D.132 Ligands: MG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.34, A:Y.34, A:N.64, A:S.125 Salt bridges: A:R.119 CDP.32: 12 residues within 4Å: Chain B: Y.34, P.63, N.64, D.111, G.115, A.118, R.119, S.124, S.125, G.128, D.132 Ligands: MG.21 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.34, B:Y.34, B:N.64, B:S.125 Salt bridges: 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
A

B
B

Membrane

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

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