SMTL ID : 6zlh.1

the structure of glutamate transporter homologue GltTk in complex with the photo switchable compound (trans)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

3 x QM5: (2~{S},3~{S})-2-azanyl-3-[[4-[2-(4-methoxyphenyl)hydrazinyl]phenyl]methoxy]butanedioic acid(Non-covalent)

QM5.1: 13 residues within 4Å: Chain A: R.278, S.279, S.280, M.314, T.317, G.360, A.361, G.362, D.398, R.401, T.402, N.405 Ligands: NA.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.278, A:R.278, A:S.280, A:G.360, A:D.398, A:N.405 Salt bridges: A:R.401 QM5.13: 14 residues within 4Å: Chain B: R.278, S.279, S.280, M.314, T.317, V.358, P.359, G.360, A.361, D.398, R.401, T.402, N.405 Ligands: NA.22 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.361 Hydrogen bonds: B:R.278, B:S.280, B:V.358, B:G.360, B:N.405 Salt bridges: B:R.401 QM5.26: 12 residues within 4Å: Chain C: R.278, S.279, S.280, M.314, T.317, G.360, A.361, D.398, R.401, T.402, N.405 Ligands: NA.32 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.278, C:R.278, C:S.280, C:T.317, C:G.360, C:N.405 Salt bridges: C:R.401

3 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.2: 8 residues within 4Å: Chain A: L.10, L.198, G.202, Q.205, R.289, E.293 Chain C: R.173 Ligands: 1PE.29 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.10, A:Q.205 Hydrogen bonds: A:L.198, A:Q.205, C:R.173 Salt bridges: A:R.289, C:R.173 DMU.17: 9 residues within 4Å: Chain A: R.173 Chain B: L.10, L.198, G.201, G.202, Q.205, Y.206, R.289, E.293 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.10, B:Q.205, B:Y.206 Hydrogen bonds: B:L.198, B:R.289, A:R.173 Salt bridges: B:R.289 DMU.27: 8 residues within 4Å: Chain B: R.173 Chain C: Y.9, L.198, G.201, G.202, Q.205, R.289, E.293 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.9 Hydrogen bonds: C:L.198, C:Q.205, C:R.289, C:R.289, B:R.173, B:R.173 Salt bridges: C:R.289

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 3 residues within 4Å: Chain A: R.107, L.108, N.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110 PG4.4: 2 residues within 4Å: Chain A: D.424, S.426 No protein-ligand interaction detected (PLIP) PG4.6: 2 residues within 4Å: Chain A: W.16, R.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.265, A:R.265

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

PGE.5: 3 residues within 4Å: Chain A: V.226, A.231, K.232 No protein-ligand interaction detected (PLIP) PGE.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.18: 3 residues within 4Å: Chain B: R.107, L.108, N.110 No protein-ligand interaction detected (PLIP) PGE.19: 5 residues within 4Å: Chain B: G.81, G.84, V.85, V.88 Ligands: PEG.16 No protein-ligand interaction detected (PLIP) PGE.28: 2 residues within 4Å: Chain B: A.78 Chain C: D.11 No protein-ligand interaction detected (PLIP)

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

NA.8: 6 residues within 4Å: Chain A: G.309, A.310, N.313, N.405, V.406, D.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.313, A:D.409 NA.9: 5 residues within 4Å: Chain A: Y.91, T.94, S.95, N.313, D.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.94, A:N.313 NA.10: 4 residues within 4Å: Chain A: S.279, S.280, S.281 Ligands: QM5.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.279, A:S.280, A:S.281 NA.20: 6 residues within 4Å: Chain B: G.309, A.310, N.313, N.405, V.406, D.409 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.280, B:S.280 NA.21: 5 residues within 4Å: Chain B: Y.91, T.94, S.95, N.313, D.315 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.91 NA.22: 4 residues within 4Å: Chain B: S.279, S.280, S.281 Ligands: QM5.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.280, B:S.281 NA.30: 6 residues within 4Å: Chain C: S.280, G.309, A.310, N.313, N.405, D.409 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.280, C:S.280 NA.31: 5 residues within 4Å: Chain C: Y.91, T.94, S.95, N.313, D.315 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.95 NA.32: 4 residues within 4Å: Chain C: S.279, S.280, S.281 Ligands: QM5.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.280, C:S.281

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

PEG.11: 8 residues within 4Å: Chain A: L.65, F.145, L.148, F.159, F.189 Chain C: F.145 Ligands: PEG.24, PEG.35 No protein-ligand interaction detected (PLIP) PEG.12: 3 residues within 4Å: Chain A: P.77, A.78, G.81 No protein-ligand interaction detected (PLIP) PEG.15: 3 residues within 4Å: Chain B: N.172, R.173, N.174 No protein-ligand interaction detected (PLIP) PEG.16: 4 residues within 4Å: Chain B: P.77, A.78, G.81 Ligands: PGE.19 No protein-ligand interaction detected (PLIP) PEG.23: 5 residues within 4Å: Chain A: K.150 Chain B: A.149, K.150 Chain C: A.149, K.150 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.150, A:K.150 PEG.24: 6 residues within 4Å: Chain A: F.145 Chain B: L.65, F.159, L.192 Ligands: PEG.11, PEG.35 No protein-ligand interaction detected (PLIP) PEG.25: 4 residues within 4Å: Chain B: G.235, Y.238, T.239, F.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.238, B:T.239 PEG.33: 4 residues within 4Å: Chain C: L.22, I.272, F.275, M.403 No protein-ligand interaction detected (PLIP) PEG.34: 3 residues within 4Å: Chain C: N.172, N.174, R.179 No protein-ligand interaction detected (PLIP) PEG.35: 5 residues within 4Å: Chain B: F.145 Chain C: L.148, F.159 Ligands: PEG.11, PEG.24 No protein-ligand interaction detected (PLIP) PEG.36: 4 residues within 4Å: Chain C: P.77, A.78, G.81 Ligands: 1PE.29 No protein-ligand interaction detected (PLIP) PEG.37: 2 residues within 4Å: Chain C: T.43, Y.44 No protein-ligand interaction detected (PLIP) PEG.38: 3 residues within 4Å: Chain C: R.107, L.108, N.110 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.108 PEG.39: 3 residues within 4Å: Chain C: V.234, G.235, Y.238 No protein-ligand interaction detected (PLIP)

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.29: 5 residues within 4Å: Chain C: I.161, I.162, Y.169 Ligands: DMU.2, PEG.36 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arkhipova, V. et al., Structural Aspects of Photopharmacology: Insight into the Binding of Photoswitchable and Photocaged Inhibitors to the Glutamate Transporter Homologue. J.Am.Chem.Soc. (2021)

Release Date

2021-01-27

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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