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

Crystal structure of ThiT complexed with LMG116

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

BNG.1: 6 residues within 4Å: Chain A: V.31, Y.32, I.35, W.138, W.141 Ligands: BNG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.31, A:V.31, A:Y.32, A:Y.32, A:I.35 Hydrogen bonds: A:Y.32, A:Y.32 Water bridges: A:K.139 BNG.2: 6 residues within 4Å: Chain A: K.139, G.140, W.141, A.145 Ligands: BNG.1, PEG.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.141, A:W.141, A:A.145 Hydrogen bonds: A:W.141 Water bridges: A:W.141 BNG.3: 4 residues within 4Å: Chain A: A.15, A.19, F.22, L.66 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.19, A:F.22, A:F.22 BNG.4: 6 residues within 4Å: Chain A: L.97, F.98, R.99, P.109, V.116 Ligands: BNG.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.97 Water bridges: A:K.101 BNG.5: 9 residues within 4Å: Chain A: F.98, A.108, P.109, L.111, L.112, F.115, F.163 Ligands: BNG.4, PEG.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.108, A:L.111, A:L.112, A:F.115, A:F.163

1 x 26G: 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}ethanol(Non-covalent)

26G.6: 12 residues within 4Å: Chain A: W.34, I.36, E.38, E.84, Y.85, H.125, G.129, W.133, Y.146, V.150, N.151 Ligands: PG4.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.36, A:Y.85, A:W.133, A:W.133, A:Y.146, A:V.150 Hydrogen bonds: A:H.125, A:N.151 Water bridges: A:N.29, A:Y.74 pi-Stacking: A:H.125, A:W.133

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

PG4.7: 3 residues within 4Å: Chain A: T.54, L.57 Ligands: P6G.24 No protein-ligand interaction detected (PLIP) PG4.8: 3 residues within 4Å: Chain A: F.163, I.167, K.171 No protein-ligand interaction detected (PLIP) PG4.9: 7 residues within 4Å: Chain A: T.30, G.33, W.34, I.36, Y.74 Ligands: 26G.6, PEG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.34 Water bridges: A:S.154

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

PEG.10: 5 residues within 4Å: Chain A: M.68, L.78, F.82, L.86 Ligands: 1PE.22 No protein-ligand interaction detected (PLIP) PEG.11: 4 residues within 4Å: Chain A: Y.74, L.76, Y.136 Ligands: PG4.9 No protein-ligand interaction detected (PLIP) PEG.12: 3 residues within 4Å: Chain A: L.112, V.116 Ligands: BNG.5 No protein-ligand interaction detected (PLIP) PEG.13: 3 residues within 4Å: Chain A: L.157, I.160 Ligands: P6G.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.157 PEG.14: 6 residues within 4Å: Chain A: P.28, N.29, T.30, V.37, I.39 Ligands: P6G.26 No protein-ligand interaction detected (PLIP) PEG.15: 3 residues within 4Å: Chain A: V.144, L.148 Ligands: BNG.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.145 PEG.16: 5 residues within 4Å: Chain A: F.173, P.174, K.175, L.176 Ligands: PEG.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.175 PEG.17: 3 residues within 4Å: Chain A: L.119, F.123 Ligands: P6G.25 No protein-ligand interaction detected (PLIP) PEG.18: 3 residues within 4Å: Chain A: F.173 Ligands: PEG.16, P6G.26 No protein-ligand interaction detected (PLIP) PEG.19: 2 residues within 4Å: Chain A: I.131 Ligands: PEG.20 No protein-ligand interaction detected (PLIP) PEG.20: 2 residues within 4Å: Chain A: I.130 Ligands: PEG.19 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.134, A:S.134 PEG.21: 2 residues within 4Å: Chain A: L.11, T.54 No protein-ligand interaction detected (PLIP)

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

1PE.22: 6 residues within 4Å: Chain A: M.68, I.69, T.70, G.71, I.75 Ligands: PEG.10 No protein-ligand interaction detected (PLIP)

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

PG0.23: 4 residues within 4Å: Chain A: I.23, L.26, I.27, P.28 No protein-ligand interaction detected (PLIP)

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

P6G.24: 8 residues within 4Å: Chain A: L.53, L.57, V.87, V.90, S.91, I.94, L.120 Ligands: PG4.7 No protein-ligand interaction detected (PLIP) P6G.25: 9 residues within 4Å: Chain A: F.115, L.119, Y.122, F.123, F.126, L.148, G.155, I.156 Ligands: PEG.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.115 P6G.26: 9 residues within 4Å: Chain A: L.20, I.24, I.42, L.46, I.165, F.169 Ligands: PEG.13, PEG.14, PEG.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swier, L.J.Y.M. et al., Crystal structures of ThiT with small molecule modulators. To be Published

Release Date

2014-08-27

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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