SMTL ID : 8jez.1

Human sodium-dependent vitamin C transporter 1 in an apo inward-open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.60 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 1 residues within 4Å: Chain A: N.144 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.144 No protein-ligand interaction detected (PLIP)

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

AV0.2: 9 residues within 4Å: Chain A: Y.284 Chain B: Y.474, N.478, G.480, A.481, N.483, T.484, L.493 Ligands: LBN.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.484, B:L.493 Hydrogen bonds: B:N.478, B:N.483, B:N.483 AV0.4: 14 residues within 4Å: Chain A: L.219, I.222, L.223, F.224, Y.227, L.228, N.230, L.231, F.252 Chain B: L.507, I.510, L.511, T.514 Ligands: LBN.3 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.219, A:L.223, A:Y.227, A:Y.227, A:Y.227, B:L.507, B:L.511, B:T.514 Hydrogen bonds: A:N.230 AV0.9: 9 residues within 4Å: Chain A: Y.474, N.478, G.480, A.481, N.483, T.484, L.493 Chain B: Y.284 Ligands: LBN.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.484, A:L.493 Hydrogen bonds: A:N.478, A:N.483, A:N.483 AV0.11: 14 residues within 4Å: Chain A: L.507, I.510, L.511, T.514 Chain B: L.219, I.222, L.223, F.224, Y.227, L.228, N.230, L.231, F.252 Ligands: LBN.10 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.219, B:L.223, B:Y.227, B:Y.227, B:Y.227, A:L.507, A:L.511, A:T.514 Hydrogen bonds: B:N.230

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

LBN.3: 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, A.481, I.482, L.507 Ligands: AV0.2, AV0.4 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.211, A:W.211, A:W.211, A:A.215, A:A.215, A:I.218, A:L.219, B:F.463, B:F.467, B:L.471, B:I.482, B:L.507 Salt bridges: A:H.210 LBN.10: 15 residues within 4Å: Chain A: F.463, F.467, L.471, A.481, I.482, L.507 Chain B: H.210, W.211, G.212, A.215, I.218, L.219, Y.284 Ligands: AV0.9, AV0.11 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.211, B:W.211, B:W.211, B:A.215, B:A.215, B:I.218, B:L.219, A:F.463, A:F.467, A:L.471, A:I.482, A:L.507 Salt bridges: B:H.210

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 10 residues within 4Å: Chain A: M.262, T.263, W.265, L.266, Y.269, T.290, D.295, M.297, L.419, S.422 9 PLIP interactions: 9 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:T.290, A:L.419 CLR.6: 12 residues within 4Å: Chain A: I.183, T.187, T.191, L.322, F.325, S.326, L.329, A.330, F.502, G.505, C.506, F.509 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.183, A:T.187, A:T.191, A:L.322, A:L.329, A:L.329, A:A.330, A:F.502, A:F.509 CLR.12: 10 residues within 4Å: Chain B: M.262, T.263, W.265, L.266, Y.269, T.290, D.295, M.297, L.419, S.422 9 PLIP interactions: 9 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:T.290, B:L.419 CLR.13: 12 residues within 4Å: Chain B: I.183, T.187, T.191, L.322, F.325, S.326, L.329, A.330, F.502, G.505, C.506, F.509 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.183, B:T.187, B:T.191, B:L.322, B:L.329, B:L.329, B:A.330, B:F.502, B:F.509

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.7: 10 residues within 4Å: Chain A: I.96, V.100, R.358, F.361, T.362, I.365, F.546, V.553, I.564, C.565 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.96, A:I.96, A:V.100, A:R.358, A:F.361, A:I.365, A:I.365, A:F.546, A:I.564, A:I.564 PLM.14: 10 residues within 4Å: Chain B: I.96, V.100, R.358, F.361, T.362, I.365, F.546, V.553, I.564, C.565 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.96, B:I.96, B:V.100, B:R.358, B:F.361, B:I.365, B:I.365, B:F.546, B:I.564, B:I.564

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, T.A. et al., Cryo-EM structures of human sodium-dependent vitamin C transporter 1. To Be Published

Release Date

2024-06-19

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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