SMTL ID : 3tdk.2 (1 other biounit)

Crystal Structure of Human UDP-Glucose Dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 21 residues within 4Å: Chain A: I.10, G.11, A.12, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, S.88, V.89, N.90, T.91, Y.108, S.130, T.131, V.132, S.275, K.279, R.346 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.14, A:V.15, A:V.37, A:N.90, A:T.131, A:V.132, A:V.132, A:S.275, A:R.346 Water bridges: A:G.13, A:G.16, A:R.41 Salt bridges: A:R.41, A:R.346, A:R.346 pi-Stacking: A:Y.108 NAD.3: 20 residues within 4Å: Chain B: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, S.88, V.89, N.90, T.91, Y.108, C.112, S.130, T.131, V.132, S.275, K.279, R.346 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:A.12, B:Y.14, B:V.15, B:V.37, B:R.41, B:N.90, B:T.91, B:T.91, B:T.91, B:S.130, B:T.131, B:V.132, B:S.275, B:K.279 Water bridges: B:R.41, B:N.90, B:A.111, B:T.131, B:R.346 Salt bridges: B:R.41, B:R.346, B:R.346 pi-Stacking: B:Y.108 NAD.5: 18 residues within 4Å: Chain C: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, S.88, V.89, N.90, T.91, Y.108, S.130, T.131, V.132, K.279, R.346 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.14, C:V.15, C:V.37, C:R.41, C:N.90, C:T.131, C:V.132, C:V.132 Salt bridges: C:R.41, C:R.346, C:R.346 NAD.7: 18 residues within 4Å: Chain D: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, S.88, V.89, N.90, T.91, Y.108, T.131, V.132, E.165, K.279, R.346 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.14, D:V.15, D:V.37, D:R.41, D:N.90, D:T.131, D:V.132, D:V.132, D:E.165, D:S.275 Salt bridges: D:R.346, D:R.346 pi-Stacking: D:Y.108 NAD.9: 20 residues within 4Å: Chain E: G.11, A.12, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, S.88, V.89, N.90, T.91, Y.108, S.130, T.131, V.132, E.165, K.279, R.346 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:A.12, E:G.13, E:G.13, E:Y.14, E:V.15, E:V.37, E:N.38, E:N.90, E:T.91, E:T.131, E:V.132, E:V.132 Water bridges: E:G.16 Salt bridges: E:R.41, E:R.346, E:R.346 pi-Stacking: E:Y.108 NAD.11: 19 residues within 4Å: Chain F: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, S.88, V.89, N.90, T.91, Y.108, S.130, T.131, V.132, S.275, K.279, R.346 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:Y.14, F:V.15, F:V.37, F:R.41, F:V.89, F:N.90, F:T.91, F:T.91, F:T.131, F:K.279 Water bridges: F:G.13, F:G.16 Salt bridges: F:R.41, F:R.346, F:R.346 pi-Stacking: F:Y.108

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

UPG.2: 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 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.231 Hydrogen bonds: A:F.162, 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 Salt bridges: A:K.339, A:K.339 pi-Stacking: A:F.265 UPG.4: 22 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, R.442 21 PLIP interactions: 2 interactions with chain A, 19 interactions with chain B Hydrogen bonds: A:R.260, A:R.260, B:T.131, B:F.162, B:E.165, B:K.220, B:K.267, B:K.267, B:S.269, B:G.273, B:F.338, B:R.442, B:R.442 Hydrophobic interactions: B:I.231 Water bridges: B:G.273, B:C.276, B:K.339, B:K.339, B:E.416 Salt bridges: B:K.339 pi-Stacking: B:F.265 UPG.6: 22 residues within 4Å: Chain C: 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, R.442 Chain D: R.260 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.231, C:F.265 Hydrogen bonds: C:E.165, C:K.220, C:K.220, C:N.224, C:K.267, C:K.267, C:S.269, C:G.273, C:F.338, C:R.442, C:R.442, D:R.260, D:R.260 Salt bridges: C:K.339 UPG.8: 22 residues within 4Å: Chain C: R.260 Chain D: 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, R.442 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.231 Hydrogen bonds: D:E.165, D:K.220, D:K.220, D:K.267, D:K.267, D:S.269, D:G.273, D:F.338, D:R.442, D:R.442, C:R.260, C:R.260 Water bridges: D:E.416 Salt bridges: D:K.339 pi-Stacking: D:F.265 UPG.10: 22 residues within 4Å: Chain E: 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, R.442 Chain F: R.260 19 PLIP interactions: 2 interactions with chain F, 17 interactions with chain E Hydrogen bonds: F:R.260, F:R.260, E:T.131, E:E.161, E:E.165, E:K.220, E:K.267, E:K.267, E:S.269, E:G.273, E:F.338, E:R.442, E:R.442 Hydrophobic interactions: E:I.231 Water bridges: E:R.177, E:E.416, E:E.416 Salt bridges: E:K.339, E:K.339 UPG.12: 22 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, L.227, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, F.338, K.339, R.442 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:I.231, F:F.265 Hydrogen bonds: F:T.131, F:E.165, F:K.220, F:N.224, 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

Rajakannan, V. et al., Structural Basis of Cooperativity in Human UDP-Glucose Dehydrogenase. Plos One (2011)

Release Date

2011-10-26

Peptides

UDP-glucose 6-dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

D
K

E
J

F
I

UDP-glucose 6-dehydrogenase

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