SMTL ID : 3vtf.1

Structure of a UDP-glucose dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.1: 21 residues within 4Å: Chain A: Y.31, E.175, F.176, L.177, R.178, E.179, K.228, N.232, I.239, Y.273, F.274, G.275, G.279, F.280, G.281, C.284, F.285, F.343, K.344, R.427 Chain B: R.268 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.239, A:Y.273 Hydrogen bonds: A:F.176, A:E.179, A:K.228, A:N.232, A:Y.273, A:Y.273, A:G.275, A:G.275, A:G.281, A:F.343, A:R.427, B:R.268, B:R.268 Water bridges: A:T.145, A:T.145, A:G.279, A:C.284, A:R.427 Salt bridges: A:K.344, A:K.344 UPG.3: 21 residues within 4Å: Chain A: R.268 Chain B: Y.31, E.175, F.176, L.177, R.178, E.179, K.228, N.232, I.239, Y.273, F.274, G.275, G.279, F.280, G.281, C.284, F.285, F.343, K.344, R.427 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.239, B:Y.273 Hydrogen bonds: B:F.176, B:E.179, B:K.228, B:N.232, B:Y.273, B:Y.273, B:Y.273, B:G.275, B:G.275, B:G.281, B:F.343, B:R.427, A:R.268, A:R.268 Water bridges: B:T.145, B:G.279, B:C.284, B:R.427 Salt bridges: B:K.344, B:K.344

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: G.420, K.436 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain B: G.420, K.436 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakuraba, H. et al., Structure of a UDP-glucose dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum. Acta Crystallogr.,Sect.F (2012)

Release Date

2012-09-19

Peptides

UDP-glucose 6-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-glucose 6-dehydrogenase