SMTL ID : 8jew.1

Human sodium-dependent vitamin C transporter 1 bound to L-ascorbic acid in an inward-open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.49 Å

Oligo State

homo-dimer

Ligands

2 x ASC: ASCORBIC ACID(Non-covalent)

ASC.1: 14 residues within 4Å: Chain A: C.55, T.59, A.109, S.110, A.111, F.112, E.334, T.380, S.381, S.382, S.383, P.384 Ligands: NA.2, NA.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:C.55, A:S.110, A:F.112, A:E.334, A:S.383 Water bridges: A:A.113, A:T.380 ASC.11: 14 residues within 4Å: Chain B: C.55, T.59, A.109, S.110, A.111, F.112, E.334, T.380, S.381, S.382, S.383, P.384 Ligands: NA.12, NA.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:C.55, B:S.110, B:F.112, B:E.334, B:S.383 Water bridges: B:A.113, B:T.380

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

NA.2: 5 residues within 4Å: Chain A: E.334, D.338, S.381, S.383 Ligands: ASC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.381 NA.3: 6 residues within 4Å: Chain A: G.58, V.62, S.110, A.111, F.112 Ligands: ASC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.58 NA.12: 5 residues within 4Å: Chain B: E.334, D.338, S.381, S.383 Ligands: ASC.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.338 NA.13: 6 residues within 4Å: Chain B: G.58, V.62, S.110, A.111, F.112 Ligands: ASC.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.110

4 x AV0: Lauryl Maltose Neopentyl Glycol(Non-covalent)

AV0.4: 10 residues within 4Å: Chain A: Y.284 Chain B: Y.474, N.478, G.480, A.481, N.483, T.484, G.485, L.493 Ligands: LBN.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.493 Hydrogen bonds: B:Y.474, B:N.483 AV0.6: 13 residues within 4Å: Chain A: L.219, L.223, Y.227, L.228, N.230, L.231, F.252 Chain B: L.507, I.510, L.511, T.514, P.516 Ligands: LBN.5 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.507, B:L.511, B:T.514, A:L.219, A:L.223, A:Y.227, A:Y.227 AV0.14: 10 residues within 4Å: Chain A: Y.474, N.478, G.480, A.481, N.483, T.484, G.485, L.493 Chain B: Y.284 Ligands: LBN.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.493 Hydrogen bonds: A:Y.474, A:N.483 AV0.16: 13 residues within 4Å: Chain A: L.507, I.510, L.511, T.514, P.516 Chain B: L.219, L.223, Y.227, L.228, N.230, L.231, F.252 Ligands: LBN.15 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.219, B:L.223, B:Y.227, B:Y.227, A:L.507, A:L.511, A:T.514

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

LBN.5: 15 residues within 4Å: Chain A: H.210, W.211, G.212, A.215, I.218, L.219, Y.284 Chain B: F.463, F.467, L.471, L.475, A.481, L.507 Ligands: AV0.4, AV0.6 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.463, B:F.467, B:L.471, B:L.475, B:L.507, A:W.211, A:W.211, A:W.211, A:W.211, A:A.215, A:I.218, A:L.219 Salt bridges: A:H.210 LBN.15: 15 residues within 4Å: Chain A: F.463, F.467, L.471, L.475, A.481, L.507 Chain B: H.210, W.211, G.212, A.215, I.218, L.219, Y.284 Ligands: AV0.14, AV0.16 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.463, A:F.467, A:L.471, A:L.475, A:L.507, B:W.211, B:W.211, B:W.211, B:W.211, B:A.215, B:I.218, B:L.219 Salt bridges: B:H.210

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 8 residues within 4Å: Chain A: M.262, T.263, W.265, L.266, Y.269, T.290, D.295, L.419 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:M.262, A:W.265, A:W.265, A:W.265, A:L.266, A:Y.269, A:Y.269, A:Y.269, A:Y.269, A:T.290, A:L.419 Hydrogen bonds: A:D.295 CLR.8: 11 residues within 4Å: Chain A: I.183, T.187, T.191, L.322, F.325, L.329, L.496, F.502, G.505, C.506, F.509 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.183, A:I.183, A:T.187, A:T.191, A:L.322, A:F.325, A:F.325, A:L.329, A:L.329, A:L.496, A:F.502, A:F.502, A:F.509, A:F.509 Hydrogen bonds: A:T.191 CLR.17: 8 residues within 4Å: Chain B: M.262, T.263, W.265, L.266, Y.269, T.290, D.295, L.419 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:M.262, B:W.265, B:W.265, B:W.265, B:L.266, B:Y.269, B:Y.269, B:Y.269, B:Y.269, B:T.290, B:L.419 Hydrogen bonds: B:D.295 CLR.18: 11 residues within 4Å: Chain B: I.183, T.187, T.191, L.322, F.325, L.329, L.496, F.502, G.505, C.506, F.509 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.183, B:I.183, B:T.187, B:T.191, B:L.322, B:F.325, B:F.325, B:L.329, B:L.329, B:L.496, B:F.502, B:F.502, B:F.509, B:F.509 Hydrogen bonds: B:T.191

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.9: 1 residues within 4Å: Chain A: N.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.144, A:N.144 NAG.19: 1 residues within 4Å: Chain B: N.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.144, B:N.144

2 x PLM: PALMITIC ACID(Covalent)

PLM.10: 10 residues within 4Å: Chain A: I.96, V.100, F.361, T.362, I.365, F.546, V.553, L.559, I.564, C.565 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.96, A:V.100, A:F.361, A:I.365, A:L.559, A:I.564 PLM.20: 10 residues within 4Å: Chain B: I.96, V.100, F.361, T.362, I.365, F.546, V.553, L.559, I.564, C.565 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.96, B:V.100, B:F.361, B:I.365, B:L.559, B:I.564

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, T.A. et al., Dimeric transport mechanism of human vitamin C transporter SVCT1. Nat Commun (2024)

Release Date

2024-05-22

Peptides

Solute carrier family 23 member 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Solute carrier family 23 member 1

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