SMTL ID : 5dwy.1

Crystal structure of a substrate-free glutamate transporter homologue GltTk

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

11 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 5 residues within 4Å: Chain A: Y.238, M.271, F.275, M.403 Ligands: PGE.2 No protein-ligand interaction detected (PLIP) PGE.2: 2 residues within 4Å: Chain A: I.245 Ligands: PGE.1 No protein-ligand interaction detected (PLIP) PGE.3: 5 residues within 4Å: Chain A: L.30, H.34, G.223, V.226, V.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.34 PGE.4: 3 residues within 4Å: Chain A: G.81, G.84 Ligands: PGE.5 No protein-ligand interaction detected (PLIP) PGE.5: 3 residues within 4Å: Chain A: P.77, G.81 Ligands: PGE.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.81 PGE.6: 7 residues within 4Å: Chain A: T.135, N.138, E.152, V.153, L.154, P.155, G.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.135, A:N.138, A:V.153, A:L.154 PGE.16: 8 residues within 4Å: Chain B: T.135, N.138, V.153, L.154, P.155, G.354, T.355 Ligands: PEG.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.153, B:L.154 PGE.17: 4 residues within 4Å: Chain B: L.30, M.219, G.223, V.226 No protein-ligand interaction detected (PLIP) PGE.26: 5 residues within 4Å: Chain C: P.77, A.78, G.81 Ligands: PEG.12, PEG.30 No protein-ligand interaction detected (PLIP) PGE.27: 5 residues within 4Å: Chain C: L.30, H.34, M.219, G.223, V.226 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.34 PGE.28: 8 residues within 4Å: Chain A: K.57, V.60, A.149, S.281 Chain C: T.142, N.143, A.146, K.150 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.142, C:N.143, C:K.150, C:K.150

23 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: T.142, N.143 Chain B: K.57, G.151, S.281 Ligand excluded by PLIP PEG.8: 3 residues within 4Å: Chain A: G.202, Q.205 Ligands: PEG.30 Ligand excluded by PLIP PEG.9: 3 residues within 4Å: Chain A: S.74, D.298, E.422 Ligand excluded by PLIP PEG.10: 2 residues within 4Å: Chain A: K.254, D.259 Ligand excluded by PLIP PEG.11: 5 residues within 4Å: Chain A: A.149, K.150 Chain B: A.149, K.150 Chain C: A.149 Ligand excluded by PLIP PEG.12: 3 residues within 4Å: Chain A: L.10 Ligands: PGE.26, PEG.30 Ligand excluded by PLIP PEG.13: 5 residues within 4Å: Chain A: M.171, N.172, R.173, N.174, R.179 Ligand excluded by PLIP PEG.14: 1 residues within 4Å: Chain A: G.201 Ligand excluded by PLIP PEG.18: 4 residues within 4Å: Chain B: L.22, I.264, K.268, I.272 Ligand excluded by PLIP PEG.19: 2 residues within 4Å: Chain B: T.43, Y.44 Ligand excluded by PLIP PEG.20: 4 residues within 4Å: Chain B: I.162, Y.169 Ligands: PEG.23, BOG.25 Ligand excluded by PLIP PEG.21: 1 residues within 4Å: Chain B: K.86 Ligand excluded by PLIP PEG.22: 5 residues within 4Å: Chain B: T.135, L.154, I.312, G.354 Ligands: PGE.16 Ligand excluded by PLIP PEG.23: 4 residues within 4Å: Chain B: Y.169 Chain C: L.198 Ligands: PEG.20, PEG.35 Ligand excluded by PLIP PEG.24: 4 residues within 4Å: Chain B: V.133 Chain C: T.43, Y.44, F.48 Ligand excluded by PLIP PEG.29: 2 residues within 4Å: Chain C: G.81, G.84 Ligand excluded by PLIP PEG.30: 4 residues within 4Å: Chain C: Y.169 Ligands: PEG.8, PEG.12, PGE.26 Ligand excluded by PLIP PEG.31: 4 residues within 4Å: Chain B: S.181 Chain C: L.186, R.187, D.190 Ligand excluded by PLIP PEG.32: 4 residues within 4Å: Chain C: D.298, K.421, E.422, L.423 Ligand excluded by PLIP PEG.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PEG.34: 5 residues within 4Å: Chain C: K.86, Y.90, L.252, F.256, T.419 Ligand excluded by PLIP PEG.35: 3 residues within 4Å: Chain C: G.201, G.202 Ligands: PEG.23 Ligand excluded by PLIP PEG.36: 5 residues within 4Å: Chain C: T.135, N.138, L.154, G.354, T.355 Ligand excluded by PLIP

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.15: 5 residues within 4Å: Chain A: R.82, K.86, F.256, I.415, T.419 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.86, A:I.415, A:T.419 Hydrogen bonds: A:T.419 Salt bridges: A:K.86 BOG.25: 6 residues within 4Å: Chain B: P.77, A.78, G.81, F.304 Chain C: R.7 Ligands: PEG.20 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.77, B:F.304 Hydrogen bonds: C:R.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guskov, A. et al., Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk. Nat Commun (2016)

Release Date

2016-09-28

Peptides

Proton/glutamate symporter, SDF family: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Proton/glutamate symporter, SDF family

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