SMTL ID : 6c58.1

Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-xylose bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

10 x UDX: URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE(Non-covalent)

UDX.1: 19 residues within 4Å: Chain A: G.11, 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 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:V.89, A:Y.108 Hydrogen bonds: A:Y.14, A:V.15, A:V.37, A:R.41, A:R.41, A:T.91, A:T.91, A:S.130, A:S.130, A:T.131, A:T.131, A:V.132, A:S.275, A:K.279 Water bridges: A:G.13, A:G.16, A:N.38, A:R.41, A:N.90, A:N.90, A:E.165, A:R.346 Salt bridges: A:R.41, A:R.346, A:R.346, A:R.346 pi-Stacking: A:Y.108 UDX.2: 22 residues within 4Å: Chain A: 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 B: R.260 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.231, A:F.265 Hydrogen bonds: A:F.162, A:E.165, A:K.220, A:K.267, A:K.267, A:S.269, A:G.273, A:G.273, A:F.338, A:R.442, A:R.442, B:R.260, B:R.260 Water bridges: A:C.276, A:F.277, A:K.339, A:K.339, A:K.339, A:K.339, A:K.339 Salt bridges: A:K.339, A:K.339 UDX.4: 18 residues within 4Å: Chain B: G.11, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, V.89, N.90, T.91, Y.108, S.130, T.131, V.132, S.275, K.279, R.346 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:Y.108 Hydrogen bonds: B:Y.14, B:V.15, B:V.37, B:N.38, B:R.41, B:R.41, B:T.91, B:T.91, B:S.130, B:S.130, B:T.131, B:T.131, B:V.132, B:S.275 Water bridges: B:G.13, B:G.16, B:R.41 Salt bridges: B:R.41, B:R.346, B:R.346, B:R.346 UDX.5: 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 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.231, B:F.265 Hydrogen bonds: B:F.162, B:E.165, B:K.220, B:K.267, B:K.267, B:S.269, B:G.273, B:G.273, B:F.338, B:R.442, B:R.442, A:R.260, A:R.260 Water bridges: B:F.265, B:C.276, B:K.339, B:K.339, B:K.339 Salt bridges: B:K.339, B:K.339 UDX.7: 19 residues within 4Å: Chain C: G.11, 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 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:V.89, C:Y.108 Hydrogen bonds: C:Y.14, C:V.15, C:V.37, C:R.41, C:T.91, C:T.91, C:S.130, C:T.131, C:T.131, C:V.132, C:S.275, C:K.279 Water bridges: C:G.13, C:G.16, C:R.41, C:S.130, C:E.165, C:R.346 Salt bridges: C:R.41, C:R.346, C:R.346, C:R.346 pi-Stacking: C:Y.108 UDX.8: 23 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, E.416, R.442 Chain D: R.260 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.231, C:F.265 Hydrogen bonds: C:F.162, C:E.165, C:K.220, C:K.267, C:K.267, C:S.269, C:G.273, C:G.273, C:E.416, C:R.442, C:R.442, D:R.260, D:R.260 Water bridges: C:F.265, C:C.276, C:F.277, C:K.339 Salt bridges: C:K.339, C:K.339 UDX.9: 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 23 PLIP interactions: 21 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.231, D:F.265 Hydrogen bonds: D:F.162, D:E.165, D:K.220, D:K.267, D:K.267, D:S.269, D:G.273, D:G.273, D:E.416, D:R.442, D:R.442, C:R.260, C:R.260 Water bridges: D:L.163, D:C.276, D:K.339, D:K.339, D:K.339, D:K.339 Salt bridges: D:K.339, D:K.339 UDX.11: 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 23 PLIP interactions: 21 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:I.231 Hydrogen bonds: E:F.162, E:E.165, E:K.220, E:K.267, E:K.267, E:S.269, E:G.273, E:G.273, E:F.338, E:R.442, E:R.442, F:R.260, F:R.260 Water bridges: E:L.163, E:E.165, E:C.276, E:C.276, E:C.276, E:K.339 Salt bridges: E:K.339, E:K.339 pi-Stacking: E:F.265 UDX.12: 18 residues within 4Å: Chain F: G.11, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, V.89, N.90, T.91, Y.108, S.130, T.131, V.132, S.275, K.279, R.346 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:V.89, F:Y.108 Hydrogen bonds: F:Y.14, F:V.15, F:V.37, F:N.38, F:R.41, F:R.41, F:T.91, F:T.91, F:S.130, F:T.131, F:V.132, F:S.275 Water bridges: F:R.41, F:R.41 Salt bridges: F:R.41, F:R.346, F:R.346, F:R.346 UDX.13: 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 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:I.231, F:F.265 Hydrogen bonds: F:F.162, F:E.165, F:K.220, F:K.267, F:K.267, F:S.269, F:G.273, F:G.273, F:F.338, F:R.442, F:R.442, E:R.260, E:R.260 Water bridges: F:C.276, F:K.339, F:K.339 Salt bridges: F:K.339, F:K.339

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: M.358, Q.390 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: M.358, Q.390 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain D: M.358, Q.390 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gross, P.G. et al., The A225L Substitution of hUGDH alters structure and function. To Be Published

Release Date

2019-01-16

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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