SMTL ID : 7qoa.1 (1 other biounit)

Structure of CodB, a cytosine transporter in an outward-facing conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x CYT: 6-AMINOPYRIMIDIN-2(1H)-ONE(Non-covalent)

CYT.1: 8 residues within 4Å: Chain A: F.33, Q.105, W.108, S.203, F.204, S.206, A.207, T.279 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.33, A:F.204, A:T.279 Hydrogen bonds: A:Q.105, A:Q.105, A:Q.105, A:S.206, A:A.207 pi-Stacking: A:W.108, A:W.108

1 x PEF: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PEF.2: 3 residues within 4Å: Chain A: W.363, L.367, L.402 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.363, A:W.363, A:L.367

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.3: 15 residues within 4Å: Chain A: W.38, T.39, G.41, A.42, P.119, A.123, G.251, M.252, A.253, D.254, S.256, D.257, I.260, I.269, L.272 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.119, A:P.119, A:A.123, A:D.254, A:I.260, A:I.269, A:I.269, A:L.272 Hydrogen bonds: A:G.251, A:A.253, A:D.257 Water bridges: A:D.254, A:D.254

2 x A6L: 2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

A6L.4: 7 residues within 4Å: Chain A: G.44, L.47, F.49, F.53, L.182, V.185, A.244 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.49, A:F.49, A:F.53, A:L.182, A:L.182, A:V.185, A:A.244 A6L.5: 3 residues within 4Å: Chain A: W.95, I.294, T.295 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.95, A:W.95

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 6 residues within 4Å: Chain A: G.29, L.30, F.32, N.275, T.278, T.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.29, A:T.279, A:T.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hatton, C.E. et al., Structure of cytosine transport protein CodB provides insight into nucleobase-cation symporter 1 mechanism. Embo J. (2022)

Release Date

2022-07-13

Peptides

Cytosine permease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Cytosine permease

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