SMTL ID : 8tz5.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x U56: N-hydroxycytidine(Non-covalent)

U56.1: 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.467 Hydrogen bonds: A:Q.362, A:E.364, A:S.395, A:Y.400, A:E.540, A:N.586, A:S.589 pi-Stacking: A:F.584 U56.7: 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.467 Hydrogen bonds: B:Q.362, B:E.364, B:S.395, B:Y.400, B:E.540, B:N.586, B:S.589 pi-Stacking: B:F.584 U56.13: 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 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.467 Hydrogen bonds: C:Q.362, C:E.364, C:S.395, C:Y.400, C:E.540, C:N.586, C:S.589 pi-Stacking: C:F.584

3 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:I.360 NA.8: 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:I.360 NA.14: 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:N.357

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

LBN.3: 17 residues within 4Å: Chain A: W.199, L.202, I.203, V.206, W.209, L.210, F.225, V.245, Y.246, W.247, R.248, F.251, I.254, G.255, F.258, M.632 Ligands: LBN.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.199, A:W.199, A:W.199, A:L.202, A:V.206, A:F.225, A:F.251, A:I.254, A:F.258, A:F.258, A:F.258 Hydrogen bonds: A:V.245, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.199, A:L.202, A:V.206, A:W.209, A:F.251, A:W.252, A:F.258, A:F.258, A:L.262 Hydrogen bonds: A:W.199, A:Y.246, A:Y.246, A:Y.246 Salt bridges: A:R.248 LBN.5: 12 residues within 4Å: Chain A: Q.280, V.281, T.283, F.284, Y.287, F.316, V.319, L.323 Chain B: F.484, S.487, A.488, W.491 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.488, A:Q.280, A:F.284, A:F.316 Hydrogen bonds: A:Y.287 LBN.6: 14 residues within 4Å: Chain A: L.234, T.235, F.238, K.240, F.428, F.514, F.587, M.613, R.614, L.616, I.617, T.620, I.621, F.624 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.238, A:F.238, A:F.428, A:F.514, A:I.617, A:I.617 Hydrogen bonds: A:R.614 Salt bridges: A:R.614 LBN.9: 17 residues within 4Å: Chain B: W.199, L.202, I.203, V.206, W.209, L.210, F.225, V.245, Y.246, W.247, R.248, F.251, I.254, G.255, F.258, M.632 Ligands: LBN.10 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.199, B:W.199, B:W.199, B:L.202, B:V.206, B:F.225, B:F.251, B:I.254, B:F.258, B:F.258, B:F.258 Hydrogen bonds: B:V.245, 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.199, B:L.202, B:V.206, B:W.209, B:F.251, B:W.252, B:F.258, B:F.258, B:L.262 Hydrogen bonds: B:W.199, B:Y.246, B:Y.246, B:Y.246 Salt bridges: B:R.248 LBN.11: 12 residues within 4Å: Chain B: 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.280, B:F.284, B:F.316 Hydrogen bonds: B:Y.287 LBN.12: 14 residues within 4Å: Chain B: L.234, T.235, F.238, K.240, F.428, F.514, F.587, M.613, R.614, L.616, I.617, T.620, I.621, F.624 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.238, B:F.238, B:F.428, B:F.514, B:I.617, B:I.617 Hydrogen bonds: B:R.614 Salt bridges: B:R.614 LBN.15: 17 residues within 4Å: Chain C: W.199, L.202, I.203, V.206, W.209, L.210, F.225, V.245, Y.246, W.247, R.248, F.251, I.254, G.255, F.258, M.632 Ligands: LBN.16 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.199, C:W.199, C:W.199, C:L.202, C:V.206, C:F.225, C:F.251, C:I.254, C:F.258, C:F.258, C:F.258 Hydrogen bonds: C:V.245, C:W.247 LBN.16: 17 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, L.256, F.258, L.259, L.262 Ligands: LBN.15 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.199, C:L.202, C:V.206, C:W.209, C:F.251, C:W.252, C:F.258, C:F.258, C:L.262 Hydrogen bonds: C:W.199, C:Y.246, C:Y.246, C:Y.246 Salt bridges: C:R.248 LBN.17: 12 residues within 4Å: Chain A: 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: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Q.280, C:F.284, C:F.316, A:A.488 Hydrogen bonds: C:Y.287 LBN.18: 14 residues within 4Å: Chain C: L.234, T.235, F.238, K.240, F.428, F.514, F.587, M.613, R.614, L.616, I.617, T.620, I.621, F.624 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.238, C:F.238, C:F.428, C:F.514, C:I.617, C:I.617 Hydrogen bonds: C:R.614 Salt bridges: 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
B

C
C

Membrane

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

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