SMTL ID : 2qb4.2 (1 other biounit)

Crystal Structure Analysis of LeuT complexed with L-leucine, sodium and desipramine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

BOG.1: 4 residues within 4Å: Chain A: L.53, P.445, R.446, Y.448 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.53, A:Y.448, A:Y.448 Hydrogen bonds: A:R.446 Water bridges: A:I.447 BOG.2: 2 residues within 4Å: Chain A: F.167, I.170 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.167, A:F.167, A:I.170 Water bridges: A:L.166, A:L.166 BOG.3: 7 residues within 4Å: Chain A: P.164, S.165, L.166, Y.169, H.391, F.395 Ligands: BOG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.164 BOG.4: 8 residues within 4Å: Chain A: K.163, H.391, L.392, F.395 Chain B: W.484, F.488 Ligands: BOG.3, BOG.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.488, B:F.488, B:F.488, A:L.392 Hydrogen bonds: A:K.163 BOG.5: 10 residues within 4Å: Chain A: I.161, L.396 Chain B: M.476, E.477, E.478, T.479, V.483, W.484, R.487 Ligands: BOG.4 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.484, B:W.484, A:I.161, A:I.161, A:L.396 Hydrogen bonds: B:E.477, B:T.479, B:T.479, B:R.487 BOG.11: 4 residues within 4Å: Chain B: L.53, P.445, R.446, Y.448 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.53, B:Y.448, B:Y.448 Hydrogen bonds: B:R.446 Water bridges: B:I.447 BOG.12: 2 residues within 4Å: Chain B: F.167, I.170 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.167, B:F.167, B:I.170 Water bridges: B:L.166, B:L.166 BOG.13: 7 residues within 4Å: Chain B: P.164, S.165, L.166, Y.169, H.391, F.395 Ligands: BOG.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.164 BOG.14: 8 residues within 4Å: Chain A: W.484, F.488 Chain B: K.163, H.391, L.392, F.395 Ligands: BOG.13, BOG.15 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.392, A:F.488, A:F.488, A:F.488 Hydrogen bonds: B:K.163 BOG.15: 10 residues within 4Å: Chain A: M.476, E.477, E.478, T.479, V.483, W.484, R.487 Chain B: I.161, L.396 Ligands: BOG.14 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.161, B:I.161, B:L.396, A:W.484, A:W.484 Hydrogen bonds: A:E.477, A:T.479, A:R.487

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

NA.6: 6 residues within 4Å: Chain A: G.20, V.23, G.24, A.351, T.354, S.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.20 NA.7: 7 residues within 4Å: Chain A: A.22, V.23, G.24, N.27, T.254, N.286 Ligands: LEU.8 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.24, A:N.27, A:T.254, A:N.286, L.8, L.8 NA.16: 6 residues within 4Å: Chain B: G.20, V.23, G.24, A.351, T.354, S.355 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.354, B:T.354 NA.17: 7 residues within 4Å: Chain B: A.22, V.23, G.24, N.27, T.254, N.286 Ligands: LEU.18 7 PLIP interactions: 4 interactions with chain B, 3 Ligand-Ligand interactions Hydrogen bonds: B:G.24, B:N.27, B:T.254, B:N.286, L.18, L.18, L.18

2 x LEU: LEUCINE(Non-covalent)

LEU.8: 14 residues within 4Å: Chain A: N.21, A.22, G.24, L.25, G.26, N.27, Y.108, F.253, T.254, S.256, F.259, S.355, I.359 Ligands: NA.7 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.108, A:F.253, A:F.259 Hydrogen bonds: A:G.24, A:G.26, A:N.27, A:T.254, A:S.256, A:S.256, L.8 LEU.18: 14 residues within 4Å: Chain B: N.21, A.22, G.24, L.25, G.26, N.27, Y.108, F.253, T.254, S.256, F.259, S.355, I.359 Ligands: NA.17 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.108, B:F.253, B:F.259 Hydrogen bonds: B:G.24, B:G.26, B:N.27, B:Y.108, B:T.254, B:T.254, B:S.256, B:S.256, L.18

4 x DSM: 3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE(Non-covalent)

DSM.9: 13 residues within 4Å: Chain A: L.25, L.29, R.30, V.33, Q.34, Y.107, I.111, F.253, A.319, F.320, L.400, D.401, D.404 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.25, A:L.29, A:R.30, A:V.33, A:V.33, A:Y.107, A:I.111, A:F.253, A:A.319, A:F.320 Hydrogen bonds: A:D.401 Water bridges: A:A.319 DSM.10: 8 residues within 4Å: Chain A: I.178, S.181, R.185, G.190, R.193, F.194, I.197, F.350 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.178, A:R.193, A:F.194, A:I.197, A:F.350 pi-Stacking: A:F.194, A:F.194 DSM.19: 13 residues within 4Å: Chain B: L.25, L.29, R.30, V.33, Q.34, Y.107, I.111, F.253, A.319, F.320, L.400, D.401, D.404 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.25, B:L.29, B:R.30, B:V.33, B:V.33, B:Y.107, B:I.111, B:F.253, B:A.319, B:F.320 Hydrogen bonds: B:D.401 Water bridges: B:A.319 DSM.20: 8 residues within 4Å: Chain B: I.178, S.181, R.185, G.190, R.193, F.194, I.197, F.350 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.178, B:R.193, B:F.194, B:I.197, B:F.350 pi-Stacking: B:F.194, B:F.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, S.K. et al., Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature (2007)

Release Date

2007-08-21

Peptides

Transporter: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Transporter

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