SMTL ID : 4pop.2 (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: 11 residues within 4Å: Chain A: W.44, I.46, E.48, E.94, Y.95, Y.132, H.135, G.139, W.143, Y.156, N.161 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.44, A:Y.95, A:W.143, A:W.143, A:Y.156 Hydrogen bonds: A:H.135, A:N.161 Water bridges: A:K.131 pi-Stacking: A:W.44, A:H.135, A:W.143

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

PG0.2: 7 residues within 4Å: Chain A: M.78, I.85, L.88, A.91, F.92, L.96 Ligands: 1PE.21 No protein-ligand interaction detected (PLIP)

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

BNG.3: 7 residues within 4Å: Chain A: F.108, P.119, L.122, F.125 Ligands: BNG.4, PEG.5, PG4.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.122, A:F.125 BNG.4: 7 residues within 4Å: Chain A: L.107, F.108, R.109, P.119, V.126 Ligands: BNG.3, PEG.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.126 Water bridges: A:K.111

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

PEG.5: 5 residues within 4Å: Chain A: A.118, L.122, F.173 Ligands: BNG.3, PEG.12 No protein-ligand interaction detected (PLIP) PEG.6: 3 residues within 4Å: Chain A: V.47, I.170 Ligands: PG4.20 No protein-ligand interaction detected (PLIP) PEG.7: 3 residues within 4Å: Chain A: Y.42, W.148, W.151 No protein-ligand interaction detected (PLIP) PEG.8: 2 residues within 4Å: Chain A: F.136 Ligands: PG4.17 No protein-ligand interaction detected (PLIP) PEG.9: 2 residues within 4Å: Ligands: PEG.15, PG4.18 No protein-ligand interaction detected (PLIP) PEG.10: 4 residues within 4Å: Chain A: L.63, V.97, S.101, I.104 No protein-ligand interaction detected (PLIP) PEG.11: 5 residues within 4Å: Chain A: V.126, L.129, L.130, F.133 Ligands: BNG.4 No protein-ligand interaction detected (PLIP) PEG.12: 2 residues within 4Å: Chain A: L.121 Ligands: PEG.5 No protein-ligand interaction detected (PLIP) PEG.13: 3 residues within 4Å: Chain A: I.34, I.49, I.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.49 PEG.14: 6 residues within 4Å: Chain A: N.17, R.19, L.20, R.61, H.189, N.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.20, A:R.61, A:R.61 PEG.15: 5 residues within 4Å: Chain A: T.40, G.43, W.44 Ligands: PEG.9, PG4.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.40, A:T.40

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

PG4.16: 5 residues within 4Å: Chain A: K.149, G.150, W.151, A.155, L.158 No protein-ligand interaction detected (PLIP) PG4.17: 8 residues within 4Å: Chain A: F.125, L.129, Y.132, F.133, F.136, G.162, G.165 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.125 PG4.18: 7 residues within 4Å: Chain A: T.40, G.43, W.44, I.46, Y.84 Ligands: PEG.9, PEG.15 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.39 PG4.19: 2 residues within 4Å: Chain A: V.126 Ligands: BNG.3 No protein-ligand interaction detected (PLIP) PG4.20: 4 residues within 4Å: Chain A: T.40, V.41, Y.42 Ligands: PEG.6 No protein-ligand interaction detected (PLIP)

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

1PE.21: 7 residues within 4Å: Chain A: I.75, M.78, I.79, T.80, G.81, I.85 Ligands: PG0.2 No protein-ligand interaction detected (PLIP)

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.22: 4 residues within 4Å: Chain A: A.29, F.32, I.75, L.76 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
B

Membrane

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

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