SMTL ID : 8tz2.1

Cryo-EM structure of bovine concentrative nucleoside transporter 3 in MSP2N2 nanodiscs, apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: N.357, I.360, G.361, Q.362, T.391, I.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.357 NA.2: 5 residues within 4Å: Chain A: S.390, T.391, S.417, C.582, C.623 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.417, A:C.582 NA.5: 6 residues within 4Å: Chain B: N.357, I.360, G.361, Q.362, T.391, I.392 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.357 NA.6: 5 residues within 4Å: Chain B: S.390, T.391, S.417, C.582, C.623 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.390, B:S.417 NA.9: 6 residues within 4Å: Chain C: N.357, I.360, G.361, Q.362, T.391, I.392 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.360 NA.10: 5 residues within 4Å: Chain C: S.390, T.391, S.417, C.582, C.623 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.390, C:S.417

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

LBN.3: 18 residues within 4Å: Chain A: W.199, L.202, I.203, V.206, W.209, L.210, F.225, L.228, V.245, Y.246, W.247, R.248, F.251, I.254, G.255, F.258, I.629, M.632 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.199, A:W.199, A:L.202, A:F.251, A:F.251, A:F.251, A:I.254, A:F.258, A:F.258 Hydrogen bonds: A:W.247, A:R.248 LBN.4: 12 residues within 4Å: Chain A: Q.280, V.281, T.283, F.284, Y.287, F.316, V.319, L.397 Chain C: F.484, S.487, A.488, W.491 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.284, A:F.284, A:F.284, A:F.316, C:F.484 Hydrogen bonds: A:Y.287 LBN.7: 18 residues within 4Å: Chain B: W.199, L.202, I.203, V.206, W.209, L.210, F.225, L.228, V.245, Y.246, W.247, R.248, F.251, I.254, G.255, F.258, I.629, M.632 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.199, B:W.199, B:L.202, B:F.251, B:F.251, B:F.251, B:I.254, B:F.258, B:F.258 Hydrogen bonds: B:W.247, B:R.248 LBN.8: 12 residues within 4Å: Chain A: F.484, S.487, A.488, W.491 Chain B: Q.280, V.281, T.283, F.284, Y.287, F.316, V.319, L.397 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.284, B:F.284, B:F.284, B:F.316, A:F.484 Hydrogen bonds: B:Y.287 LBN.11: 18 residues within 4Å: Chain C: W.199, L.202, I.203, V.206, W.209, L.210, F.225, L.228, V.245, Y.246, W.247, R.248, F.251, I.254, G.255, F.258, I.629, M.632 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.199, C:W.199, C:L.202, C:F.251, C:F.251, C:F.251, C:I.254, C:F.258, C:F.258 Hydrogen bonds: C:W.247, C:R.248 LBN.12: 12 residues within 4Å: Chain B: F.484, S.487, A.488, W.491 Chain C: Q.280, V.281, T.283, F.284, Y.287, F.316, V.319, L.397 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.284, C:F.284, C:F.284, C:F.316, B:F.484 Hydrogen bonds: C:Y.287

Links

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Citation

Wright, N.J. et al., Antiviral drug recognition and elevator-type transport motions of CNT3. Nat.Chem.Biol. (2024)

Release Date

2024-03-13

Peptides

Sodium/nucleoside cotransporter: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Membrane

We predict this structure to be a membrane protein.
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Sodium/nucleoside cotransporter

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