SMTL ID : 4n4d.1 (1 other biounit)

Structure of ThiT with AV-38 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x XX8: {3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}methanol(Non-covalent)

XX8.1: 11 residues within 4Å: Chain A: W.34, E.84, Y.122, H.125, A.128, G.129, W.133, Y.146, V.150, N.151, S.154 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.34, A:W.133, A:W.133, A:Y.146, A:V.150 Hydrogen bonds: A:H.125, A:N.151, A:S.154, A:S.154 pi-Stacking: A:W.34, A:W.34, A:H.125, A:W.133

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

BNG.2: 6 residues within 4Å: Chain A: I.94, L.97, F.98, R.99, P.109, V.116 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.94, A:L.97, A:F.98, A:F.98, A:V.116 Hydrogen bonds: A:R.99 BNG.3: 1 residues within 4Å: Chain A: A.15 No protein-ligand interaction detected (PLIP) BNG.4: 2 residues within 4Å: Chain A: V.31, Y.32 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.32

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

PG0.5: 6 residues within 4Å: Chain A: L.105, K.106, L.107, A.108, V.170, K.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.107, A:A.108 PG0.6: 6 residues within 4Å: Chain A: M.68, I.75, L.78, F.82, L.86 Ligands: PEG.7 No protein-ligand interaction detected (PLIP)

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

PEG.7: 2 residues within 4Å: Chain A: M.68 Ligands: PG0.6 No protein-ligand interaction detected (PLIP) PEG.8: 4 residues within 4Å: Chain A: T.54, L.57, V.58, L.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.57 PEG.9: 7 residues within 4Å: Chain A: N.29, T.30, G.33, W.34, I.36, Y.74 Ligands: PEG.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:T.30, A:Y.74 PEG.10: 5 residues within 4Å: Chain A: L.57, V.87, S.91, I.94 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.87 PEG.11: 3 residues within 4Å: Chain A: V.87, V.90 Ligands: PEG.10 No protein-ligand interaction detected (PLIP) PEG.12: 9 residues within 4Å: Chain A: S.25, N.29, W.34, I.36, E.38, I.39, A.40, Y.74 Ligands: PEG.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.29, A:V.37, A:A.40, A:Y.85

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

PG4.13: 5 residues within 4Å: Chain A: P.28, N.29, T.30, V.31, V.37 No protein-ligand interaction detected (PLIP)

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

PGE.14: 4 residues within 4Å: Chain A: G.140, W.141, G.142, A.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.142 PGE.15: 7 residues within 4Å: Chain A: Y.122, F.123, F.126, L.148, N.151, G.152 Ligands: 1PE.18 No protein-ligand interaction detected (PLIP) PGE.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.17: 4 residues within 4Å: Chain A: L.10, L.11, T.54, A.55 No protein-ligand interaction detected (PLIP)

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

1PE.18: 5 residues within 4Å: Chain A: F.115, V.118, L.119, I.156 Ligands: PGE.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swier, L.J.Y.M. et al., Structural studies on the thiamine binding protein ThiT. To be Published

Release Date

2014-09-17

Peptides

thiamine binding protein 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 binding protein ThiT

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