SMTL ID : 4pop.1 (1 other biounit)

ThiT with LMG139 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 2VY: 4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophene-2-carbaldehyde(Non-covalent)

2VY.1: 12 residues within 4Å: Chain A: W.44, E.48, E.94, Y.95, Y.132, H.135, A.138, G.139, W.143, Y.156, V.160, N.161 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.44, A:W.143, A:W.143, A:Y.156, A:V.160 Hydrogen bonds: A:E.94, A:Y.95, A:N.161 Water bridges: A:K.131 pi-Stacking: A:W.44, A:H.135, A:W.143

2 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.2: 1 residues within 4Å: Ligands: PG4.18 No protein-ligand interaction detected (PLIP) PG0.3: 6 residues within 4Å: Chain A: L.129, Y.132, F.133, F.136, L.158, G.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.132

3 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.4: 4 residues within 4Å: Chain A: M.78, I.79 Ligands: BNG.5, PG4.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.79 BNG.5: 8 residues within 4Å: Chain A: I.85, L.86, S.87, L.88, A.91, F.92, L.96 Ligands: BNG.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.85, A:L.88, A:A.91, A:F.92, A:L.96 Hydrogen bonds: A:L.88 BNG.6: 3 residues within 4Å: Chain A: L.158, A.159 Ligands: PG4.20 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.158

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

PEG.7: 5 residues within 4Å: Chain A: G.81, H.82, A.83, Y.84 Ligands: P6G.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.84 PEG.8: 3 residues within 4Å: Chain A: L.67, V.68, V.100 No protein-ligand interaction detected (PLIP) PEG.9: 2 residues within 4Å: Chain A: V.174, I.177 No protein-ligand interaction detected (PLIP) PEG.10: 1 residues within 4Å: Chain A: K.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.181 PEG.11: 2 residues within 4Å: Chain A: L.20, T.64 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.64, A:T.64, A:A.65 PEG.12: 3 residues within 4Å: Chain A: F.32, I.33, L.36 No protein-ligand interaction detected (PLIP) PEG.13: 3 residues within 4Å: Chain A: I.178, F.179 Ligands: PEG.14 No protein-ligand interaction detected (PLIP) PEG.14: 3 residues within 4Å: Chain A: F.179 Ligands: PEG.13, 1PE.21 No protein-ligand interaction detected (PLIP) PEG.15: 6 residues within 4Å: Chain A: N.39, T.40, G.43, W.44, I.46 Ligands: P6G.24 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.39, A:N.39, A:T.40, A:G.43 Water bridges: A:N.39 PEG.16: 1 residues within 4Å: Chain A: K.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.182

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

PG4.17: 7 residues within 4Å: Chain A: L.63, L.67, V.97, V.100, S.101, I.104, L.130 No protein-ligand interaction detected (PLIP) PG4.18: 1 residues within 4Å: Ligands: PG0.2 No protein-ligand interaction detected (PLIP) PG4.19: 3 residues within 4Å: Chain A: T.80, G.81 Ligands: BNG.4 No protein-ligand interaction detected (PLIP) PG4.20: 7 residues within 4Å: Chain A: G.150, W.151, G.152, A.153, V.154, A.155 Ligands: BNG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.152, A:V.154, A:A.155

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

1PE.21: 9 residues within 4Å: Chain A: M.27, L.30, I.34, I.37, I.49, I.52, L.56, F.179 Ligands: PEG.14 No protein-ligand interaction detected (PLIP) 1PE.22: 6 residues within 4Å: Chain A: I.104, L.107, F.108, V.126, L.129, L.130 No protein-ligand interaction detected (PLIP)

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

PGE.23: 5 residues within 4Å: Chain A: P.38, N.39, T.40, V.41, V.47 No protein-ligand interaction detected (PLIP)

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.24: 3 residues within 4Å: Chain A: Y.84 Ligands: PEG.7, PEG.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swier, L.J. et al., Structure-Based Design of Potent Small-Molecule Binders to the S-Component of the ECF Transporter for Thiamine. Chembiochem (2015)

Release Date

2014-09-17

Peptides

Thiamine transporter ThiT: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Thiamine transporter ThiT

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