SMTL ID : 9hjc.1

Cryo-EM structure of thiamine-bound human TPK1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x VIB: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM(Non-covalent)

VIB.1: 15 residues within 4Å: Chain A: W.202, L.204, L.214, S.216, T.217, S.218, N.219 Chain B: D.71, D.95, Q.96, D.97, H.98, T.99, K.103, Q.134 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.97, B:D.97, A:S.218, A:N.219 Hydrophobic interactions: A:W.202, A:W.202 pi-Stacking: A:W.202 VIB.3: 15 residues within 4Å: Chain A: D.71, Q.96, D.97, H.98, T.99, D.100, Q.134 Chain B: W.202, L.204, L.209, L.214, S.216, T.217, S.218, N.219 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.96, A:D.97, B:N.219 Hydrophobic interactions: B:W.202, B:W.202

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.46, D.71, F.72, D.73, S.74, D.100 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.46, A:D.73, A:D.100, A:D.100 MG.4: 6 residues within 4Å: Chain B: D.46, D.71, F.72, D.73, S.74, D.100 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.46, B:D.71, B:D.73, B:D.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabriel, F., Structural Basis of Membrane Transport and Pyrophosphorylation of Thiamine in Humans. Thesis (2024)

Release Date

2025-03-12

Peptides

Thiamine pyrophosphokinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thiamine pyrophosphokinase 1