SMTL ID : 9dh0.1

The Cryo-EM structure of recombinantly expressed hUGDH in complex with UDP-4-keto-xylose

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

4 x 01: (2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)

01.1: 21 residues within 4Å: Chain A: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, R.442 Chain B: R.260 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.265 Hydrogen bonds: A:E.165, A:K.220, A:K.267, A:K.267, A:S.269, A:G.273, A:F.338, A:R.442, A:R.442, B:R.260, B:R.260 Water bridges: A:F.162, A:A.164, A:C.276, A:C.276 Salt bridges: A:K.339, A:K.339 01.2: 21 residues within 4Å: Chain A: R.260 Chain B: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, L.227, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.265 Hydrogen bonds: B:E.165, B:K.220, B:K.267, B:K.267, B:S.269, B:G.273, B:F.338, B:R.442, A:R.260, A:R.260 Water bridges: B:C.276, B:E.416, A:D.258 Salt bridges: B:K.339, B:K.339 01.3: 21 residues within 4Å: Chain C: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, R.442 Chain D: R.260 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.265 Hydrogen bonds: C:E.165, C:K.220, C:K.267, C:K.267, C:S.269, C:G.273, C:F.338, C:R.442, D:R.260, D:R.260 Water bridges: C:C.276, C:F.277, C:E.416 Salt bridges: C:K.339, C:K.339 01.4: 21 residues within 4Å: Chain E: R.260 Chain F: T.131, E.161, F.162, L.163, A.164, E.165, K.220, N.224, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, R.442 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.265 Hydrogen bonds: F:E.165, F:K.220, F:K.267, F:K.267, F:S.269, F:G.273, F:F.338, F:R.442, F:R.442, E:R.260, E:R.260 Salt bridges: F:K.339, F:K.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Brien, J.H. et al., Cryo-EM Structure of Recombinantly Expressed hUGDH Unveils a Hidden, Alternative Allosteric Inhibitor. Biochemistry (2025)

Release Date

2025-03-05

Peptides

UDP-glucose 6-dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

UDP-glucose 6-dehydrogenase

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