SMTL ID : 8oud.1

Structure of the human neutral amino acid transporter ASCT2 in complex with nanobody 469

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: G.382, A.383, N.386, N.471, D.475 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.383 NA.2: 6 residues within 4Å: Chain A: T.384, M.387, S.425, V.426, G.427, A.428 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.428 NA.3: 5 residues within 4Å: Chain A: F.135, T.138, T.139, N.386, D.388 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.135, A:T.138 Water bridges: A:T.139, A:N.386 NA.6: 5 residues within 4Å: Chain B: G.382, A.383, N.386, N.471, D.475 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.475 NA.7: 5 residues within 4Å: Chain B: T.384, M.387, S.425, V.426, A.428 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.426 NA.8: 5 residues within 4Å: Chain B: F.135, T.138, T.139, N.386, D.388 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.138, B:D.388 Water bridges: B:T.139, B:N.386 NA.11: 6 residues within 4Å: Chain C: G.382, A.383, N.386, N.471, V.472, D.475 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.475 NA.12: 6 residues within 4Å: Chain C: T.384, M.387, S.425, V.426, G.427, A.428 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.384 NA.13: 5 residues within 4Å: Chain C: F.135, T.138, T.139, N.386, D.388 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.138, C:D.388 Water bridges: C:N.386, C:M.387

3 x ALA: ALANINE(Non-covalent)

ALA.4: 10 residues within 4Å: Chain A: S.351, S.352, S.353, M.387, A.429, G.430, I.431, D.464, T.468, N.471 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.353, A:I.431, A:D.464, A:N.471, A.4 ALA.9: 10 residues within 4Å: Chain B: S.351, S.352, S.353, M.387, A.429, G.430, I.431, D.464, T.468, N.471 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:S.353, B:I.431, B:D.464, B:N.471, A.9 ALA.14: 10 residues within 4Å: Chain C: S.351, S.352, S.353, M.387, A.429, G.430, I.431, D.464, T.468, N.471 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain C Hydrogen bonds: A.14, C:S.353, C:I.431, C:D.464, C:N.471

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 10 residues within 4Å: Chain A: I.191, F.192, V.236, V.240, V.243, R.246, K.247, I.415, V.419 Chain B: W.272 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.191, A:F.192, A:V.236, A:V.240, A:V.243, A:V.243, A:I.415, A:V.419, B:W.272, B:W.272 Salt bridges: A:R.246 Y01.10: 8 residues within 4Å: Chain B: I.191, V.236, V.240, V.243, R.246, K.247, I.415 Chain C: W.272 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.191, B:V.236, B:V.240, B:V.243, B:V.243, B:I.415, C:W.272, C:W.272 Salt bridges: B:R.246, B:K.247 Y01.15: 12 residues within 4Å: Chain A: W.272 Chain C: L.187, I.191, F.192, L.232, V.236, V.240, V.243, R.246, K.247, I.415, V.419 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.187, C:F.192, C:L.232, C:V.236, C:V.240, C:V.243, C:V.243, C:I.415, C:V.419, A:W.272, A:W.272 Hydrogen bonds: C:V.243 Salt bridges: C:R.246, C:K.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khare, S. et al., Receptor-recognition and antiviral mechanisms of retrovirus-derived human proteins. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-05-01

Peptides

Neutral amino acid transporter B(0): ABC
Nanobody 469: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Neutral amino acid transporter B(0)

Nanobody 469

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