SMTL ID : 6c5a.1

Human UDP-Glucose Dehydrogenase with UDP- Glc and NADH bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

NAI.1: 24 residues within 4Å: Chain A: 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, A.111, C.112, S.130, T.131, E.161, L.163, E.165, C.276, K.279, R.346 Ligands: UPG.2 25 PLIP interactions: 25 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: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 Water bridges: A:G.13, A:R.41, A:R.346, A:R.346 Salt bridges: A:R.41, A:R.346, A:R.346 NAI.4: 26 residues within 4Å: Chain B: 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, K.220, C.276, K.279, R.346 Ligands: UPG.5 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:V.15, B:E.161, B:L.163 Hydrogen bonds: B:Y.14, B:V.15, B:V.37, B:R.41, B:R.41, B:V.89, B:T.91, B:Y.108, B:T.131, B:T.131, B:E.165, B:K.279, B:K.279, B:R.346 Water bridges: B:G.13, B:G.16, B:R.41, B:N.90, B:S.275, B:R.346 Salt bridges: B:R.41, B:R.346, B:R.346 NAI.7: 26 residues within 4Å: Chain C: 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, C.112, S.130, T.131, E.161, L.163, E.165, S.275, C.276, K.279, R.346 Ligands: UPG.8 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:V.15, C:E.161, C:L.163 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 Water bridges: C:G.13, C:G.16, C:R.41, C:R.346, C:R.346, C:R.346 Salt bridges: C:R.41, C:R.346, C:R.346 NAI.10: 27 residues within 4Å: Chain D: 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, L.163, E.165, K.220, S.275, C.276, K.279, R.346 Ligands: UPG.11 22 PLIP interactions: 22 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:V.89, D:T.91, D:Y.108, D:T.131, D:E.165, D:E.165, D:S.275, D:K.279, D:K.279, D:R.346 Water bridges: D:G.13, D:G.16, D:T.131 Salt bridges: D:R.41, D:R.346 NAI.12: 25 residues within 4Å: Chain E: I.10, G.11, A.12, G.13, Y.14, V.15, D.36, V.37, R.41, 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 Ligands: UPG.13 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:V.15, E:E.161 Hydrogen bonds: E:A.12, E:Y.14, E:V.15, E:V.37, E:R.41, E:V.89, E:N.90, E:T.91, E:Y.108, E:T.131, E:E.165, E:E.165, E:S.275, E:K.279, E:K.279 Salt bridges: E:R.41 NAI.14: 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.15 29 PLIP interactions: 29 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:Y.108, 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:G.13, F:N.38, F:N.38, F:R.41, F:R.346, F:R.346, F:R.346 Salt bridges: F:R.41, F:R.346, F:R.346

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

UPG.2: 22 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, F.338, K.339, R.442 Chain B: R.260 Ligands: NAI.1 26 PLIP interactions: 24 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:N.224, 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:K.220, A:F.265, A:C.276, A:D.280, A:K.339, A:K.339, A:K.339, A:E.416, A:E.416 Salt bridges: A:K.339, A:K.339 UPG.5: 22 residues within 4Å: Chain A: R.260 Chain B: 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, D.280, F.338, K.339, R.442 Ligands: NAI.4 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.231, B:F.265 Hydrogen bonds: B:F.162, B:E.165, B:K.220, B:N.224, B:K.267, B:K.267, B:S.269, B:G.273, B:D.280, B:F.338, B:R.442, B:R.442, A:R.260, A:R.260 Salt bridges: B:K.339, B:K.339 Water bridges: A:D.258 UPG.8: 23 residues within 4Å: Chain C: 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 D: R.260 Ligands: NAI.7 25 PLIP interactions: 23 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:D.280, C:D.280, C:F.338, C:R.442, C:R.442, D:R.260, D:R.260 Water bridges: C:R.177, C:C.276, C:C.276, C:K.339, C:K.339, C:E.416 Salt bridges: C:K.339, C:K.339 UPG.11: 23 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, E.416, R.442 Ligands: NAI.10 24 PLIP interactions: 21 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.231 Hydrogen bonds: D:F.162, D:E.165, D:K.220, D:N.224, D:K.267, D:K.267, D:S.269, D:G.273, D:D.280, D:F.338, D:E.416, D:R.442, D:R.442, C:R.260, C:R.260 Water bridges: D:C.276, D:K.339, D:K.339, D:K.339, C:D.258 Salt bridges: D:K.339, D:K.339 pi-Stacking: D:F.265 UPG.13: 20 residues within 4Å: Chain E: 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 F: R.260 Ligands: NAI.12 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:F.265 Hydrogen bonds: E:F.162, E:E.165, E:K.220, E:N.224, E:K.267, E:K.267, E:S.269, E:G.273, E:F.338, E:R.442, E:R.442, F:R.260, F:R.260 Water bridges: E:C.276, E:C.276 Salt bridges: E:K.339 UPG.15: 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.14 23 PLIP interactions: 21 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:D.280, F:F.338, F:R.442, F:R.442, E:R.260, E:R.260 Water bridges: F:C.276, F:C.276, F:K.339, F:E.416, F:E.416 Salt bridges: F:K.339, F:K.339

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 6 residues within 4Å: Chain A: F.162, D.171, D.176, R.177 Chain B: D.258, R.260 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:D.258, A:D.171, A:D.176 Hydrogen bonds: A:D.176 DMS.6: 7 residues within 4Å: Chain A: D.258, R.260 Chain B: F.162, D.171, P.175, D.176, R.177 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.176 Salt bridges: B:D.171, B:D.176, A:D.258 DMS.9: 7 residues within 4Å: Chain C: F.162, A.164, D.171, D.176, R.177 Chain D: D.258, R.260 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Salt bridges: D:D.258, C:D.171, C:D.176 Hydrogen bonds: C:D.176 DMS.16: 7 residues within 4Å: Chain E: D.258, R.260 Chain F: F.162, A.164, D.171, D.176, R.177 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:D.176 Salt bridges: F:D.171, F:D.176, E:D.258

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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