SMTL ID : 8tz3.1

Cryo-EM structure of bovine concentrative nucleoside transporter 3 in complex with GS-441524, consensus reconstruction

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, G.388, T.391, I.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.360 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.390, A:S.417 NA.7: 6 residues within 4Å: Chain B: N.357, I.360, G.361, G.388, T.391, I.392 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.392 NA.8: 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.417, B:C.582 NA.13: 6 residues within 4Å: Chain C: N.357, I.360, G.361, G.388, T.391, I.392 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.360 NA.14: 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:A.413, C:S.417

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

LBN.3: 19 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 Ligands: LBN.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.199, A:W.199, A:L.202, A:V.206, A:F.225, A:F.258, A:F.258 Hydrogen bonds: A:W.247 LBN.4: 17 residues within 4Å: Chain A: W.191, I.198, W.199, L.202, G.205, V.206, W.209, Y.246, R.248, F.251, W.252, G.255, L.256, F.258, L.259, L.262 Ligands: LBN.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.198, A:L.202, A:W.209, A:F.251, A:W.252, A:F.258 Hydrogen bonds: A:W.199, A:Y.246, A:Y.246, A:Y.246 Salt bridges: A:R.248 LBN.5: 13 residues within 4Å: Chain A: Q.280, V.281, T.283, F.284, Y.287, F.316, V.319, L.323, L.397 Chain C: F.484, S.487, A.488, W.491 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.280, A:F.284, A:F.316 LBN.6: 15 residues within 4Å: Chain A: Y.231, L.234, T.235, F.238, F.428, F.514, T.536, F.587, A.610, M.613, R.614, I.617, T.620, I.621, F.624 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.238, A:F.238, A:F.514, A:I.617, A:I.621 Hydrogen bonds: A:R.614 Salt bridges: A:R.614 LBN.9: 19 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 Ligands: LBN.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.199, B:W.199, B:L.202, B:V.206, B:F.225, B:F.258, B:F.258 Hydrogen bonds: B:W.247 LBN.10: 17 residues within 4Å: Chain B: W.191, I.198, W.199, L.202, G.205, V.206, W.209, Y.246, R.248, F.251, W.252, G.255, L.256, F.258, L.259, L.262 Ligands: LBN.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.198, B:L.202, B:W.209, B:F.251, B:W.252, B:F.258 Hydrogen bonds: B:W.199, B:Y.246, B:Y.246, B:Y.246 Salt bridges: B:R.248 LBN.11: 13 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.323, L.397 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.280, B:F.284, B:F.316 LBN.12: 15 residues within 4Å: Chain B: Y.231, L.234, T.235, F.238, F.428, F.514, T.536, F.587, A.610, M.613, R.614, I.617, T.620, I.621, F.624 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.238, B:F.238, B:F.514, B:I.617, B:I.621 Hydrogen bonds: B:R.614 Salt bridges: B:R.614 LBN.15: 19 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 Ligands: LBN.16 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.199, C:W.199, C:L.202, C:V.206, C:F.225, C:F.258, C:F.258 Hydrogen bonds: C:W.247 LBN.16: 16 residues within 4Å: Chain C: W.191, I.198, W.199, L.202, G.205, V.206, W.209, Y.246, R.248, F.251, W.252, G.255, F.258, L.259, L.262 Ligands: LBN.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.198, C:L.202, C:W.209, C:F.251, C:W.252, C:F.258 Hydrogen bonds: C:W.199, C:Y.246, C:Y.246, C:Y.246 Salt bridges: C:R.248 LBN.17: 13 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.323, L.397 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.280, C:F.284, C:F.316 LBN.18: 15 residues within 4Å: Chain C: Y.231, L.234, T.235, F.238, F.428, F.514, T.536, F.587, A.610, M.613, R.614, I.617, T.620, I.621, F.624 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.238, C:F.238, C:F.514, C:I.617, C:I.621 Hydrogen bonds: C:R.614 Salt bridges: C:R.614

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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