SMTL ID : 4pov.2 (1 other biounit)

ThiT with LMG135 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, I.46, E.48, E.94, Y.95, Y.132, H.135, G.139, W.143, Y.156, V.160, N.161 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.44, A:Y.95, A:W.143, A:W.143, A:Y.156, A:V.160 Hydrogen bonds: A:E.94, 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: 5 residues within 4Å: Chain A: T.40, G.43, W.44, I.46, Y.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.40, A:Y.84

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

PG4.3: 3 residues within 4Å: Chain A: L.20, T.64, A.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.64 PG4.4: 5 residues within 4Å: Chain A: F.125, L.129, F.133, G.162, G.165 No protein-ligand interaction detected (PLIP) PG4.5: 4 residues within 4Å: Chain A: M.78, I.79, G.81 Ligands: PEG.13 No protein-ligand interaction detected (PLIP) PG4.6: 4 residues within 4Å: Chain A: A.118, L.121, L.122 Ligands: BNG.9 No protein-ligand interaction detected (PLIP)

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

BNG.7: 4 residues within 4Å: Chain A: A.25, A.29, F.32, L.76 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.32, A:F.32 BNG.8: 7 residues within 4Å: Chain A: L.107, F.108, R.109, Q.110, P.119, V.126 Ligands: BNG.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.107, A:V.126 Water bridges: A:L.107, A:K.111 BNG.9: 6 residues within 4Å: Chain A: F.108, A.118, P.119, L.122 Ligands: PG4.6, BNG.8 No protein-ligand interaction detected (PLIP)

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

PEG.10: 2 residues within 4Å: Chain A: I.170, A.171 No protein-ligand interaction detected (PLIP) PEG.11: 3 residues within 4Å: Chain A: L.122, F.125 Ligands: PEG.12 No protein-ligand interaction detected (PLIP) PEG.12: 3 residues within 4Å: Chain A: L.122, V.126 Ligands: PEG.11 No protein-ligand interaction detected (PLIP) PEG.13: 5 residues within 4Å: Chain A: M.78, L.88, F.92, L.96 Ligands: PG4.5 No protein-ligand interaction detected (PLIP) PEG.14: 3 residues within 4Å: Chain A: F.183, P.184, K.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.185

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

1PE.15: 5 residues within 4Å: Chain A: K.149, G.150, W.151, A.155, L.158 No protein-ligand interaction detected (PLIP) 1PE.16: 5 residues within 4Å: Chain A: P.38, N.39, T.40, V.47, I.175 No protein-ligand interaction detected (PLIP)

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

CL.17: 4 residues within 4Å: Chain A: G.43, W.44, W.148, Y.156 Ligand excluded by 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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