SMTL ID : 8tz1.1

Cryo-EM structure of bovine concentrative nucleoside transporter 3 in complex with Ribavirin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x RBV: 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide(Non-covalent)

RBV.1: 17 residues within 4Å: Chain A: G.361, Q.362, T.363, E.364, A.393, S.395, V.396, Y.400, L.467, I.471, N.539, E.540, F.541, F.584, N.586, S.589, I.592 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.362, A:T.363, A:S.395, A:N.586, A:S.589 RBV.8: 17 residues within 4Å: Chain B: G.361, Q.362, T.363, E.364, A.393, S.395, V.396, Y.400, L.467, I.471, N.539, E.540, F.541, F.584, N.586, S.589, I.592 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.362, B:T.363, B:S.395, B:N.586, B:S.589 RBV.15: 17 residues within 4Å: Chain C: G.361, Q.362, T.363, E.364, A.393, S.395, V.396, Y.400, L.467, I.471, N.539, E.540, F.541, F.584, N.586, S.589, I.592 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.362, C:T.363, C:S.395, C:N.586, C:S.589

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

NA.2: 5 residues within 4Å: Chain A: N.357, I.360, G.361, T.391, I.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.357 NA.3: 5 residues within 4Å: Chain A: S.390, T.391, S.417, C.582, C.623 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.417 NA.9: 5 residues within 4Å: Chain B: N.357, I.360, G.361, T.391, I.392 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.357 NA.10: 5 residues within 4Å: Chain B: S.390, T.391, S.417, C.582, C.623 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.417 NA.16: 5 residues within 4Å: Chain C: N.357, I.360, G.361, T.391, I.392 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.391 NA.17: 5 residues within 4Å: Chain C: S.390, T.391, S.417, C.582, C.623 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.417

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

LBN.4: 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, M.632 Ligands: LBN.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.199, A:W.199, A:W.199, A:L.202, A:V.206, A:F.258, A:F.258 Hydrogen bonds: A:W.247 LBN.5: 16 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, F.258, L.259, L.262 Ligands: LBN.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.198, A:L.202, 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.6: 12 residues within 4Å: Chain A: Q.280, V.281, T.283, F.284, Y.287, F.316, V.319, L.323 Chain C: F.484, S.487, A.488, W.491 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.280, A:F.284, A:F.284, A:F.284 Hydrogen bonds: A:Y.287 LBN.7: 15 residues within 4Å: Chain A: Y.231, L.234, T.235, F.238, K.240, F.428, F.514, 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.514, A:I.617, A:I.621 Hydrogen bonds: A:K.240 Salt bridges: A:R.614, A:R.614 LBN.11: 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, M.632 Ligands: LBN.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.199, B:W.199, B:W.199, B:L.202, B:V.206, B:F.258, B:F.258 Hydrogen bonds: B:W.247 LBN.12: 16 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, F.258, L.259, L.262 Ligands: LBN.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.198, B:L.202, 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.13: 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.323 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.280, B:F.284, B:F.284, B:F.284 Hydrogen bonds: B:Y.287 LBN.14: 15 residues within 4Å: Chain B: Y.231, L.234, T.235, F.238, K.240, F.428, F.514, 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.514, B:I.617, B:I.621 Hydrogen bonds: B:K.240 Salt bridges: B:R.614, B:R.614 LBN.18: 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, M.632 Ligands: LBN.19 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.199, C:W.199, C:W.199, C:L.202, C:V.206, C:F.258, C:F.258 Hydrogen bonds: C:W.247 LBN.19: 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.18 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.198, C:L.202, 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.20: 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.323 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.280, C:F.284, C:F.284, C:F.284 Hydrogen bonds: C:Y.287 LBN.21: 15 residues within 4Å: Chain C: Y.231, L.234, T.235, F.238, K.240, F.428, F.514, 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.514, C:I.617, C:I.621 Hydrogen bonds: C:K.240 Salt bridges: C:R.614, C:R.614

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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