SMTL ID : 3usp.2 (1 other biounit)

Crystal structure of LeuT in heptyl-beta-D-Selenoglucoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 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:S.355 NA.2: 6 residues within 4Å: Chain A: A.22, V.23, N.27, T.254, N.286 Ligands: LEU.4 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.4, L.4 NA.14: 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.15: 6 residues within 4Å: Chain B: A.22, V.23, N.27, T.254, N.286 Ligands: LEU.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.24, B:N.27, B:T.254, B:T.254, B:N.286

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

CL.3: 4 residues within 4Å: Chain A: K.121, Y.151, S.165 Ligands: 05L.8 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: K.121, Y.151, S.165 Ligands: 05L.21 Ligand excluded by PLIP

2 x LEU: LEUCINE(Non-covalent)

LEU.4: 15 residues within 4Å: Chain A: N.21, A.22, G.24, L.25, G.26, N.27, V.104, Y.108, F.253, T.254, S.256, F.259, S.355, I.359 Ligands: NA.2 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:V.104, A:F.253, A:F.259, A:I.359 Hydrogen bonds: A:G.24, A:G.26, A:N.27, A:T.254, A:S.256, A:S.256, A:S.355, L.4 LEU.17: 15 residues within 4Å: Chain B: N.21, A.22, G.24, L.25, G.26, N.27, V.104, Y.108, F.253, T.254, S.256, F.259, S.355, I.359 Ligands: NA.15 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.104, B:F.253, B:F.259, B:I.359 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, B:S.355, L.17

18 x 05L: heptyl 1-seleno-beta-D-glucopyranoside(Non-covalent)(Non-functional Binders)

05L.5: 8 residues within 4Å: Chain A: K.163, H.391, L.392, F.395 Chain B: W.484, F.488 Ligands: 05L.6, 05L.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.391, A:F.395, B:W.484, B:F.488 Hydrogen bonds: A:K.163 05L.6: 7 residues within 4Å: Chain A: E.159, I.161, F.395 Chain B: T.479, W.481, W.484 Ligands: 05L.5 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.481, B:W.484, B:W.484, A:I.161, A:I.161 Hydrogen bonds: B:T.479, B:T.479, A:E.159 Water bridges: B:W.481 05L.7: 8 residues within 4Å: Chain A: P.164, S.165, L.166, Y.169, F.388, H.391, F.395 Ligands: 05L.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.169, A:F.388 Hydrogen bonds: A:P.164 05L.8: 8 residues within 4Å: Chain A: I.120, K.121, V.124, L.126, F.147, F.167 Ligands: CL.3, 05L.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.120, A:V.124, A:F.167 Hydrogen bonds: A:K.121, A:L.126 05L.9: 3 residues within 4Å: Chain A: P.445, R.446, Y.448 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.445 Hydrogen bonds: A:R.446 05L.10: 11 residues within 4Å: Chain A: L.25, L.29, R.30, Q.34, I.111, F.253, A.319, F.320, L.400, D.401, D.404 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.25, A:L.29, A:I.111, A:F.253, A:A.319, A:F.320 Hydrogen bonds: A:Q.34, A:D.401 05L.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 05L.12: 4 residues within 4Å: Chain A: I.120, F.167, I.170 Ligands: 05L.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.120, A:F.167, A:F.167 Water bridges: A:L.166, A:F.167 05L.13: 2 residues within 4Å: Chain B: Y.489 Ligands: 05L.26 No protein-ligand interaction detected (PLIP) 05L.18: 8 residues within 4Å: Chain A: W.484, F.488 Chain B: K.163, H.391, L.392, F.395 Ligands: 05L.19, 05L.20 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.391, B:F.395, A:W.484, A:F.488 Hydrogen bonds: B:K.163 05L.19: 7 residues within 4Å: Chain A: T.479, W.481, W.484 Chain B: E.159, I.161, F.395 Ligands: 05L.18 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.161, B:I.161, A:W.481, A:W.484, A:W.484 Hydrogen bonds: B:E.159, A:T.479 Water bridges: A:W.481 05L.20: 8 residues within 4Å: Chain B: P.164, S.165, L.166, Y.169, F.388, H.391, F.395 Ligands: 05L.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.169, B:F.388 Hydrogen bonds: B:P.164 05L.21: 8 residues within 4Å: Chain B: I.120, K.121, V.124, L.126, F.147, F.167 Ligands: CL.16, 05L.25 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.120, B:V.124, B:F.167 Hydrogen bonds: B:K.121, B:L.126 05L.22: 3 residues within 4Å: Chain B: P.445, R.446, Y.448 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.445 Hydrogen bonds: B:R.446 05L.23: 11 residues within 4Å: Chain B: L.25, L.29, R.30, Q.34, I.111, F.253, A.319, F.320, L.400, D.401, D.404 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.25, B:L.29, B:I.111, B:F.253, B:A.319, B:F.320 Hydrogen bonds: B:Q.34, B:D.401 05L.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 05L.25: 4 residues within 4Å: Chain B: I.120, F.167, I.170 Ligands: 05L.21 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.120, B:F.167, B:F.167 Water bridges: B:L.166, B:F.167 05L.26: 2 residues within 4Å: Chain A: Y.489 Ligands: 05L.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structures of LeuT in bicelles define conformation and substrate binding in a membrane-like context. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-01-11

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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