SMTL ID : 4pov.1 (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, E.48, E.94, Y.95, K.131, Y.132, H.135, A.138, G.139, W.143, Y.156, N.161 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.44, 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: 2 residues within 4Å: Chain A: K.149, G.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.150

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

PG4.3: 7 residues within 4Å: Chain A: L.30, I.34, I.52, P.53, L.56, F.179 Ligands: PEG.13 No protein-ligand interaction detected (PLIP) PG4.4: 4 residues within 4Å: Chain A: P.38, N.39, T.40, V.47 No protein-ligand interaction detected (PLIP) PG4.5: 3 residues within 4Å: Chain A: L.67, V.97, S.101 No protein-ligand interaction detected (PLIP) PG4.6: 5 residues within 4Å: Chain A: Y.132, L.158, N.161, G.162 Ligands: 1PE.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.161 PG4.7: 8 residues within 4Å: Chain A: S.35, I.37, N.39, T.40, G.43, W.44, I.46, Y.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.37 Water bridges: A:N.39, A:N.39

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

BNG.8: 5 residues within 4Å: Chain A: K.149, G.150, W.151, G.152, A.155 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.151 Hydrogen bonds: A:G.150, A:G.152 BNG.9: 9 residues within 4Å: Chain A: M.78, I.85, L.86, S.87, L.88, A.91, F.92, L.96 Ligands: BNG.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.88, A:A.91, A:F.92, A:L.96 Hydrogen bonds: A:L.88 BNG.10: 4 residues within 4Å: Chain A: I.75, M.78, I.79 Ligands: BNG.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.75, A:I.75, A:M.78, A:I.79

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

PEG.11: 2 residues within 4Å: Chain A: A.29, F.32 No protein-ligand interaction detected (PLIP) PEG.12: 1 residues within 4Å: Chain A: I.178 No protein-ligand interaction detected (PLIP) PEG.13: 4 residues within 4Å: Chain A: M.27, R.60, L.186 Ligands: PG4.3 No protein-ligand interaction detected (PLIP) PEG.14: 4 residues within 4Å: Chain A: T.64, L.67, V.68, L.71 No protein-ligand interaction detected (PLIP) PEG.15: 3 residues within 4Å: Chain A: K.116, L.117, A.118 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.116, A:L.117, A:A.118 Water bridges: A:L.115, A:K.116, A:K.181

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

1PE.16: 6 residues within 4Å: Chain A: A.155, L.158, A.159, G.162, I.166 Ligands: PG4.6 No protein-ligand interaction detected (PLIP)

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

PGE.17: 4 residues within 4Å: Chain A: A.118, P.119, L.122 Ligands: PGE.19 No protein-ligand interaction detected (PLIP) PGE.18: 4 residues within 4Å: Chain A: L.20, I.24, T.64, R.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.109 Water bridges: A:L.63, A:T.64, A:T.64, A:T.64 PGE.19: 5 residues within 4Å: Chain A: L.107, F.108, R.109, P.119 Ligands: PGE.17 No protein-ligand interaction detected (PLIP)

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

P6G.20: 0 residues within 4Å: (No contacts) 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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