SMTL ID : 6c5z.1

Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-glucose and NADH bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-hexamer

Ligands

5 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 26 residues within 4Å: Chain A: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, I.75, S.88, V.89, N.90, T.91, Y.108, A.111, S.130, T.131, E.161, L.163, E.165, K.220, S.275, C.276, K.279, R.346 Ligands: UPG.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.15, A:E.161 Hydrogen bonds: A:Y.14, A:V.15, A:V.37, A:R.41, A:V.89, A:T.91, A:Y.108, A:T.131, A:T.131, A:E.165, A:E.165, A:S.275, A:K.279, A:K.279, A:R.346 Salt bridges: A:R.41, A:R.346, A:R.346 NAI.4: 25 residues within 4Å: Chain C: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, R.41, I.75, S.88, V.89, N.90, T.91, Y.108, A.111, C.112, S.130, T.131, E.161, L.163, E.165, C.276, K.279, R.346 Ligands: UPG.5 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:V.15, C:E.161 Hydrogen bonds: C:Y.14, C:V.15, C:V.37, C:R.41, C:R.41, C:V.89, C:T.91, C:Y.108, C:T.131, C:T.131, C:E.165, C:S.275, C:K.279, C:K.279, C:R.346 Salt bridges: C:R.41, C:R.346, C:R.346 NAI.6: 27 residues within 4Å: Chain D: I.10, G.11, A.12, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, I.75, S.88, V.89, N.90, T.91, Y.108, S.130, T.131, E.161, L.163, E.165, K.220, S.275, C.276, K.279, R.346 Ligands: UPG.7 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:V.15, D:E.161 Hydrogen bonds: D:A.12, D:Y.14, D:V.15, D:V.37, D:R.41, D:T.91, D:T.131, D:E.165, D:E.165, D:S.275, D:K.279, D:K.279, D:R.346, D:R.346 Water bridges: D:G.13, D:G.13, D:R.41, D:R.41 Salt bridges: D:R.41 NAI.8: 24 residues within 4Å: Chain E: I.10, 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, A.111, C.112, S.130, T.131, E.161, E.165, K.220, C.276, K.279 Ligands: UPG.9 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:V.15 Hydrogen bonds: E:Y.14, E:V.15, E:V.37, E:R.41, E:T.91, E:T.91, E:Y.108, E:T.131, E:E.165, E:E.165, E:K.279 Water bridges: E:R.346 Salt bridges: E:R.41 NAI.10: 26 residues within 4Å: Chain F: I.10, G.11, G.13, Y.14, V.15, D.36, V.37, N.38, R.41, I.75, S.88, V.89, N.90, T.91, Y.108, A.111, S.130, T.131, E.161, L.163, E.165, S.275, C.276, K.279, R.346 Ligands: UPG.11 25 PLIP interactions: 25 interactions with chain F Hydrophobic interactions: F:V.15, F:E.161, F:L.163 Hydrogen bonds: F:Y.14, F:V.15, F:V.37, F:R.41, F:R.41, F:V.89, F:T.91, F:T.131, F:T.131, F:E.165, F:S.275, F:K.279, F:K.279, F:R.346 Water bridges: F:G.13, F:R.41, F:R.41, F:S.275, F:R.346 Salt bridges: F:R.41, F:R.346, F:R.346

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

UPG.2: 23 residues within 4Å: Chain A: 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, D.280, F.338, K.339, R.442 Chain B: R.260 Ligands: NAI.1 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.265 Hydrogen bonds: A:F.162, A:E.165, A:K.220, A:N.224, A:K.267, A:K.267, A:S.269, A:G.273, A:D.280, A:F.338, A:R.442, A:R.442, B:R.260, B:R.260 Water bridges: A:R.177, A:F.277 Salt bridges: A:K.339 UPG.3: 18 residues within 4Å: Chain A: R.260 Chain B: E.161, F.162, K.220, N.224, I.231, F.265, L.266, K.267, S.269, F.272, G.273, C.276, F.277, D.280, F.338, K.339, R.442 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.265 Hydrogen bonds: B:F.162, B:K.220, B:K.267, B:K.267, B:S.269, B:G.273, B:F.338, B:R.442, B:R.442, A:R.260, A:R.260 Salt bridges: B:K.339, B:K.339 UPG.5: 21 residues within 4Å: Chain C: 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 Ligands: NAI.4 18 PLIP interactions: 16 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: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 Water bridges: C:K.339 Salt bridges: C:K.339, C:K.339 UPG.7: 22 residues within 4Å: Chain C: R.260 Chain D: 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 Ligands: NAI.6 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.265 Hydrogen bonds: D:F.162, D:E.165, D:E.165, D:K.220, D:K.267, D:K.267, D:S.269, D:G.273, D:F.338, D:E.416, D:R.442, D:R.442, C:R.260, C:R.260 Salt bridges: D:K.339, D:K.339 UPG.9: 19 residues within 4Å: Chain E: F.162, L.163, 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 F: R.260 Ligands: NAI.8 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:F.162, E:E.165, E:K.220, E:N.224, E:L.266, E:K.267, E:K.267, E:S.269, E:G.273, E:F.338, E:R.442, F:R.260, F:R.260 Water bridges: E:F.265, E:C.276 Salt bridges: E:K.339, E:K.339 UPG.11: 21 residues within 4Å: Chain E: R.260 Chain F: 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 Ligands: NAI.10 24 PLIP interactions: 22 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: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 Water bridges: F:R.177, F:K.220, F:C.276, F:C.276, F:D.280, F:K.339, F:E.416 Salt bridges: F:K.339, F:K.339

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

2019-01-23

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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