SMTL ID : 1ub0.1

Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: R.27, F.28, Y.236, R.239, A.258 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.27 Salt bridges: A:R.27, A:R.239 SO4.8: 5 residues within 4Å: Chain B: R.27, F.28, Y.236, R.239, A.258 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.27 Salt bridges: B:R.27, B:R.239

4 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.2: 3 residues within 4Å: Chain A: M.1, G.29 Chain B: W.257 No protein-ligand interaction detected (PLIP) DIO.3: 2 residues within 4Å: Chain A: E.56, E.90 No protein-ligand interaction detected (PLIP) DIO.9: 3 residues within 4Å: Chain A: W.257 Chain B: M.1, G.29 No protein-ligand interaction detected (PLIP) DIO.10: 2 residues within 4Å: Chain B: E.56, E.90 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: L.52, L.53, P.54, P.55, D.81, A.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.52 GOL.5: 3 residues within 4Å: Chain A: V.47, V.50 Ligands: GOL.7 No protein-ligand interaction detected (PLIP) GOL.6: 3 residues within 4Å: Chain A: P.99, L.220, R.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.224 Water bridges: A:L.226 GOL.7: 3 residues within 4Å: Chain A: V.50, G.80 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.80 GOL.11: 6 residues within 4Å: Chain B: L.52, L.53, P.54, P.55, D.81, A.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.52 GOL.12: 3 residues within 4Å: Chain B: V.47, V.50 Ligands: GOL.14 No protein-ligand interaction detected (PLIP) GOL.13: 3 residues within 4Å: Chain B: P.99, L.220, R.224 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.224 Water bridges: B:L.226 GOL.14: 3 residues within 4Å: Chain B: V.50, G.80 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kambaru, A. et al., Crystal structure of 4-amino-5-hydroxymethyl-2-methyl pyrimidine phosphate kinase (HMPP kinase) from Thermus thermophilus HB8. Eur.Biophys.J. (2025)

Release Date

2003-04-08

Peptides

Phosphomethylpyrimidine Kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphomethylpyrimidine Kinase