SMTL ID : 8jf1.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.85 Å

Oligo State

homo-dimer

Ligands

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

AV0.1: 22 residues within 4Å: Chain A: H.210, I.213, S.217, L.220, V.264, L.267, C.268, L.271, L.277, Y.284, G.285, Q.287, A.288, A.292, R.293, P.426, I.427 Chain B: N.473, E.476, S.477 Ligands: AV0.3, AV0.11 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.220, A:V.264, A:L.267, A:L.267, A:L.271, A:L.277, A:Y.284, A:A.288, A:P.426, A:I.427 Hydrogen bonds: A:H.210, A:Q.287, B:S.477 Salt bridges: A:H.210, A:H.210, A:R.293 AV0.2: 21 residues within 4Å: Chain A: D.30, L.32, L.219, I.221, I.222, L.223, Q.226, R.229, K.253, I.257, G.390, I.391, T.392, K.393, T.434 Chain B: T.189, S.193, L.444, L.447 Ligands: Y01.4, Y01.5 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.219, A:I.221, A:I.222, A:I.222, A:L.223, A:I.257, A:I.391, A:I.391, A:T.434, B:T.189, B:L.444, B:L.447 Hydrogen bonds: A:D.30, A:R.229, A:T.392, A:K.393 Salt bridges: A:R.229, A:R.229, A:K.393 AV0.3: 29 residues within 4Å: Chain A: F.200, Q.201, A.203, G.204, D.205, R.206, A.207, G.208, S.209, H.210, W.211, C.433, F.436 Chain B: F.200, Q.201, G.204, D.205, R.206, A.207, G.208, S.209, W.211, C.433, F.436 Ligands: AV0.1, Y01.4, AV0.9, AV0.11, Y01.12 20 PLIP interactions: 7 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:F.200, B:F.200, B:W.211, B:F.436, B:F.436, A:F.200, A:F.200, A:F.200, A:F.200, A:F.200, A:A.203, A:W.211, A:W.211, A:F.436, A:F.436 Hydrogen bonds: B:G.208, B:G.208, A:G.208, A:S.209, A:S.209 AV0.9: 22 residues within 4Å: Chain A: N.473, E.476, S.477 Chain B: H.210, I.213, S.217, L.220, V.264, L.267, C.268, L.271, L.277, Y.284, G.285, Q.287, A.288, A.292, R.293, P.426, I.427 Ligands: AV0.3, AV0.11 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.220, B:V.264, B:L.267, B:L.267, B:L.271, B:L.277, B:Y.284, B:A.288, B:P.426, B:I.427 Hydrogen bonds: B:H.210, B:Q.287, A:S.477 Salt bridges: B:H.210, B:H.210, B:R.293 AV0.10: 21 residues within 4Å: Chain A: T.189, S.193, L.444, L.447 Chain B: D.30, L.32, L.219, I.221, I.222, L.223, Q.226, R.229, K.253, I.257, G.390, I.391, T.392, K.393, T.434 Ligands: Y01.12, Y01.13 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.219, B:I.221, B:I.222, B:I.222, B:L.223, B:I.257, B:I.391, B:I.391, B:T.434, A:T.189, A:L.444, A:L.447 Hydrogen bonds: B:D.30, B:R.229, B:T.392, B:K.393 Salt bridges: B:R.229, B:R.229, B:K.393 AV0.11: 29 residues within 4Å: Chain A: F.200, Q.201, G.204, D.205, R.206, A.207, G.208, S.209, W.211, C.433, F.436 Chain B: F.200, Q.201, A.203, G.204, D.205, R.206, A.207, G.208, S.209, H.210, W.211, C.433, F.436 Ligands: AV0.1, AV0.3, Y01.4, AV0.9, Y01.12 20 PLIP interactions: 13 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.200, B:F.200, B:F.200, B:F.200, B:F.200, B:A.203, B:W.211, B:W.211, B:F.436, B:F.436, A:F.200, A:F.200, A:W.211, A:F.436, A:F.436 Hydrogen bonds: B:G.208, B:S.209, B:S.209, A:G.208, A:G.208

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 19 residues within 4Å: Chain A: S.214, A.215, I.218, I.222, L.345, I.386, G.387, I.391, G.430, C.433, T.434, G.437, M.438, A.441, S.445 Ligands: AV0.2, AV0.3, Y01.5, AV0.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.218, A:I.218, A:I.222, A:I.386, A:T.434, A:A.441 Y01.5: 7 residues within 4Å: Chain A: L.219, G.390, K.393 Chain B: L.197, L.444 Ligands: AV0.2, Y01.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.219, A:L.219, B:L.197, B:L.444 Salt bridges: A:K.393, A:K.393 Y01.12: 19 residues within 4Å: Chain B: S.214, A.215, I.218, I.222, L.345, I.386, G.387, I.391, G.430, C.433, T.434, G.437, M.438, A.441, S.445 Ligands: AV0.3, AV0.10, AV0.11, Y01.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.218, B:I.218, B:I.222, B:I.386, B:T.434, B:A.441 Y01.13: 7 residues within 4Å: Chain A: L.197, L.444 Chain B: L.219, G.390, K.393 Ligands: AV0.10, Y01.12 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.219, B:L.219, A:L.197, A:L.444 Salt bridges: B:K.393, B:K.393

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 11 residues within 4Å: Chain A: L.179, T.191, L.329, A.330, I.333, M.501, F.502, G.505, C.506, F.509, I.510 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.179, A:L.179, A:L.329, A:L.329, A:I.333, A:F.502, A:F.509, A:F.509, A:F.509, A:F.509, A:I.510 Hydrogen bonds: A:T.191 CLR.14: 11 residues within 4Å: Chain B: L.179, T.191, L.329, A.330, I.333, M.501, F.502, G.505, C.506, F.509, I.510 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.179, B:L.179, B:L.329, B:L.329, B:I.333, B:F.502, B:F.509, B:F.509, B:F.509, B:F.509, B:I.510 Hydrogen bonds: B:T.191

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

NAG.7: 2 residues within 4Å: Chain A: N.144, H.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.144 NAG.15: 2 residues within 4Å: Chain B: N.144, H.147 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.144

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.8: 12 residues within 4Å: Chain A: I.96, V.100, R.358, F.361, T.362, I.365, I.369, F.546, V.553, I.564, C.565, P.566 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.96, A:I.96, A:V.100, A:I.365, A:I.369, A:I.564 PLM.16: 12 residues within 4Å: Chain B: I.96, V.100, R.358, F.361, T.362, I.365, I.369, F.546, V.553, I.564, C.565, P.566 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.96, B:I.96, B:V.100, B:I.365, B:I.369, 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

2024-05-22

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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