SMTL ID : 8gnk.1

CryoEM structure of cytosol-facing, substrate-bound ratGAT1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.147, K.313, R.314, D.318 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.314 NAG.2: 2 residues within 4Å: Chain A: C.136, N.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.136

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: Y.49, Q.254, S.258, S.294 Ligand excluded by PLIP

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

NA.4: 2 residues within 4Å: Chain A: S.258 Ligands: ABU.5 No protein-ligand interaction detected (PLIP)

1 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.5: 9 residues within 4Å: Chain A: L.99, Y.103, F.257, G.260, L.263, S.359, T.363, A.418 Ligands: NA.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.99, A:F.257, A:L.263 Hydrogen bonds: A:F.257, A:T.363

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 7 residues within 4Å: Chain A: L.242, S.243, W.248, I.470, F.477 Ligands: CLR.8, CLR.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.248, A:I.470 CLR.7: 8 residues within 4Å: Chain A: W.98, L.167, D.168, P.170, S.400, W.495, V.499 Ligands: CLR.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.495, A:W.495, A:V.499 CLR.8: 6 residues within 4Å: Chain A: L.51, F.55, F.239, L.242, W.248 Ligands: CLR.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.51, A:F.55, A:L.242, A:W.248 CLR.9: 6 residues within 4Å: Chain A: I.469, G.473, L.476, F.477, V.480 Ligands: CLR.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.469, A:I.469, A:I.469, A:L.476, A:L.476, A:F.477, A:V.480, A:V.480 CLR.10: 8 residues within 4Å: Chain A: P.170, G.171, I.173, L.396, L.399, S.400, T.403 Ligands: CLR.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.170, A:I.173, A:T.403 CLR.11: 4 residues within 4Å: Chain A: I.216, R.220, T.223, L.338 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.216, A:T.223

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.12: 8 residues within 4Å: Chain A: F.218, V.222, T.223, L.224, P.225, G.226, I.231, F.299 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.218, A:I.231, A:F.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayak, S.R. et al., Cryo-EM structure of GABA transporter 1 reveals substrate recognition and transport mechanism. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-05-31

Peptides

Sodium- and chloride-dependent GABA transporter 1: A
Fragment antigen binding light chain: B
fragment antigen binding 9D5 heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

Membrane

We predict this structure to be a membrane protein.
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Sodium- and chloride-dependent GABA transporter 1

Fragment antigen binding light chain

fragment antigen binding 9D5 heavy chain

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