SMTL ID : 7ahk.1

Crystal structure of the outward-facing state of the substrate-free Na+-only bound glutamate transporter homolog GltPh

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: G.306, A.307, N.310, N.401, D.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.405 NA.2: 5 residues within 4Å: Chain A: Y.89, T.92, S.93, N.310, D.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.92, A:T.92 Water bridges: A:N.310 NA.21: 5 residues within 4Å: Chain B: G.306, A.307, N.310, N.401, D.405 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.306 NA.22: 5 residues within 4Å: Chain B: Y.89, T.92, S.93, N.310, D.312 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.89, B:T.92 Water bridges: B:N.310 NA.41: 5 residues within 4Å: Chain C: G.306, A.307, N.310, N.401, D.405 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.306 NA.42: 5 residues within 4Å: Chain C: Y.89, T.92, S.93, N.310, D.312 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.89, C:T.92 Water bridges: C:N.310

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

BOG.3: 14 residues within 4Å: Chain A: I.256, S.260, F.261, H.264, M.292, G.293, I.294, S.295, A.410, A.413, K.414, G.417, T.418, L.419 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.256, A:A.413 Hydrogen bonds: A:S.295, A:L.419, A:L.419 Water bridges: A:G.417 BOG.23: 14 residues within 4Å: Chain B: I.256, S.260, F.261, H.264, M.292, G.293, I.294, S.295, A.410, A.413, K.414, G.417, T.418, L.419 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.256, B:A.413 Hydrogen bonds: B:S.295, B:L.419, B:L.419 Water bridges: B:G.417 BOG.43: 14 residues within 4Å: Chain C: I.256, S.260, F.261, H.264, M.292, G.293, I.294, S.295, A.410, A.413, K.414, G.417, T.418, L.419 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.256, C:A.413 Hydrogen bonds: C:S.295, C:L.419, C:L.419 Water bridges: C:G.417

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 7 residues within 4Å: Chain A: R.276, S.277, S.278, D.394, T.398, N.401 Ligands: GOL.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.278, A:N.401 Water bridges: A:R.276 PO4.24: 7 residues within 4Å: Chain B: R.276, S.277, S.278, D.394, T.398, N.401 Ligands: GOL.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.278, B:N.401 Water bridges: B:R.276 PO4.44: 7 residues within 4Å: Chain C: R.276, S.277, S.278, D.394, T.398, N.401 Ligands: GOL.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.278, C:N.401 Water bridges: C:R.276

36 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.5: 6 residues within 4Å: Chain A: V.224, A.229, A.233, V.237, T.240 Ligands: OLC.20 Ligand excluded by PLIP LFA.6: 2 residues within 4Å: Chain A: Q.14 Ligands: LFA.16 Ligand excluded by PLIP LFA.7: 3 residues within 4Å: Chain A: I.253, Y.254 Ligands: LFA.8 Ligand excluded by PLIP LFA.8: 4 residues within 4Å: Chain A: L.91, Y.254, T.415 Ligands: LFA.7 Ligand excluded by PLIP LFA.9: 4 residues within 4Å: Chain A: V.86, L.90, I.309, I.350 Ligand excluded by PLIP LFA.10: 3 residues within 4Å: Chain B: L.53, K.196, G.200 Ligand excluded by PLIP LFA.11: 5 residues within 4Å: Chain A: I.137, I.155, F.156, I.159 Ligands: LFA.15 Ligand excluded by PLIP LFA.12: 8 residues within 4Å: Chain A: I.262, K.263, K.266, L.270, F.273, M.399 Ligands: OLC.19, OLC.20 Ligand excluded by PLIP LFA.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.14: 2 residues within 4Å: Chain A: P.206, F.210 Ligand excluded by PLIP LFA.15: 7 residues within 4Å: Chain A: P.75, G.79, G.82, V.83, I.137, A.353 Ligands: LFA.11 Ligand excluded by PLIP LFA.16: 2 residues within 4Å: Chain A: I.25 Ligands: LFA.6 Ligand excluded by PLIP LFA.25: 6 residues within 4Å: Chain B: V.224, A.229, A.233, V.237, T.240 Ligands: OLC.40 Ligand excluded by PLIP LFA.26: 2 residues within 4Å: Chain B: Q.14 Ligands: LFA.36 Ligand excluded by PLIP LFA.27: 3 residues within 4Å: Chain B: I.253, Y.254 Ligands: LFA.28 Ligand excluded by PLIP LFA.28: 4 residues within 4Å: Chain B: L.91, Y.254, T.415 Ligands: LFA.27 Ligand excluded by PLIP LFA.29: 4 residues within 4Å: Chain B: V.86, L.90, I.309, I.350 Ligand excluded by PLIP LFA.30: 3 residues within 4Å: Chain C: L.53, K.196, G.200 Ligand excluded by PLIP LFA.31: 5 residues within 4Å: Chain B: I.137, I.155, F.156, I.159 Ligands: LFA.35 Ligand excluded by PLIP LFA.32: 8 residues within 4Å: Chain B: I.262, K.263, K.266, L.270, F.273, M.399 Ligands: OLC.39, OLC.40 Ligand excluded by PLIP LFA.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.34: 2 residues within 4Å: Chain B: P.206, F.210 Ligand excluded by PLIP LFA.35: 7 residues within 4Å: Chain B: P.75, G.79, G.82, V.83, I.137, A.353 Ligands: LFA.31 Ligand excluded by PLIP LFA.36: 2 residues within 4Å: Chain B: I.25 Ligands: LFA.26 Ligand excluded by PLIP LFA.45: 6 residues within 4Å: Chain C: V.224, A.229, A.233, V.237, T.240 Ligands: OLC.60 Ligand excluded by PLIP LFA.46: 2 residues within 4Å: Chain C: Q.14 Ligands: LFA.56 Ligand excluded by PLIP LFA.47: 3 residues within 4Å: Chain C: I.253, Y.254 Ligands: LFA.48 Ligand excluded by PLIP LFA.48: 4 residues within 4Å: Chain C: L.91, Y.254, T.415 Ligands: LFA.47 Ligand excluded by PLIP LFA.49: 4 residues within 4Å: Chain C: V.86, L.90, I.309, I.350 Ligand excluded by PLIP LFA.50: 3 residues within 4Å: Chain A: L.53, K.196, G.200 Ligand excluded by PLIP LFA.51: 5 residues within 4Å: Chain C: I.137, I.155, F.156, I.159 Ligands: LFA.55 Ligand excluded by PLIP LFA.52: 8 residues within 4Å: Chain C: I.262, K.263, K.266, L.270, F.273, M.399 Ligands: OLC.59, OLC.60 Ligand excluded by PLIP LFA.53: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.54: 2 residues within 4Å: Chain C: P.206, F.210 Ligand excluded by PLIP LFA.55: 7 residues within 4Å: Chain C: P.75, G.79, G.82, V.83, I.137, A.353 Ligands: LFA.51 Ligand excluded by PLIP LFA.56: 2 residues within 4Å: Chain C: I.25 Ligands: LFA.46 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 6 residues within 4Å: Chain A: K.55, R.276, S.277, S.278, S.279 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.55, A:S.278, A:S.279 GOL.18: 4 residues within 4Å: Chain A: R.276, D.390, A.391, D.394 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.276, A:R.276, A:D.390, A:D.390 GOL.37: 6 residues within 4Å: Chain B: K.55, R.276, S.277, S.278, S.279 Ligands: PO4.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.55, B:S.278, B:S.279 GOL.38: 4 residues within 4Å: Chain B: R.276, D.390, A.391, D.394 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.276, B:R.276, B:D.390, B:D.390 GOL.57: 6 residues within 4Å: Chain C: K.55, R.276, S.277, S.278, S.279 Ligands: PO4.44 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.55, C:S.278, C:S.279 GOL.58: 4 residues within 4Å: Chain C: R.276, D.390, A.391, D.394 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.276, C:R.276, C:D.390, C:D.390

6 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.19: 4 residues within 4Å: Chain A: F.248, I.259, K.263 Ligands: LFA.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.248, A:I.259 Salt bridges: A:K.263 OLC.20: 12 residues within 4Å: Chain A: L.17, L.20, A.24, L.28, M.217, G.221, V.222, V.224, V.225, Y.236 Ligands: LFA.5, LFA.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.17, A:A.24, A:L.28, A:V.224, A:Y.236 OLC.39: 4 residues within 4Å: Chain B: F.248, I.259, K.263 Ligands: LFA.32 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.248, B:I.259 Salt bridges: B:K.263 OLC.40: 12 residues within 4Å: Chain B: L.17, L.20, A.24, L.28, M.217, G.221, V.222, V.224, V.225, Y.236 Ligands: LFA.25, LFA.32 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.17, B:A.24, B:L.28, B:V.224, B:Y.236 OLC.59: 4 residues within 4Å: Chain C: F.248, I.259, K.263 Ligands: LFA.52 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.248, C:I.259 Salt bridges: C:K.263 OLC.60: 12 residues within 4Å: Chain C: L.17, L.20, A.24, L.28, M.217, G.221, V.222, V.224, V.225, Y.236 Ligands: LFA.45, LFA.52 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.17, C:A.24, C:L.28, C:V.224, C:Y.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alleva, C. et al., Na + -dependent gate dynamics and electrostatic attraction ensure substrate coupling in glutamate transporters. Sci Adv (2020)

Release Date

2020-11-18

Peptides

Glutamate transporter homolog: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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Glutamate transporter homolog