SMTL ID : 3khu.1

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

UPG.1: 23 residues within 4Å: Chain A: Q.162, F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, D.281, F.339, K.340, R.443 Chain B: R.261 Ligands: UPG.2, EDO.5 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.232, A:F.266 Hydrogen bonds: A:Q.162, A:E.166, A:K.221, A:K.221, A:N.225, A:K.268, A:K.268, A:S.270, A:G.274, A:F.339, A:R.443, A:R.443, B:R.261, B:R.261 Water bridges: A:F.163, A:K.221, A:F.266, A:E.417 Salt bridges: A:K.340, A:K.340 UPG.2: 18 residues within 4Å: Chain A: I.11, G.12, G.14, Y.15, V.16, D.37, V.38, R.42, S.89, V.90, N.91, S.131, T.132, Q.162, S.276, C.277, R.347 Ligands: UPG.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.11, A:V.38 Hydrogen bonds: A:Y.15, A:V.16, A:R.42, A:S.131, A:S.131, A:T.132, A:T.132, A:Q.162, A:S.276, A:S.276, A:R.347, A:R.347 Water bridges: A:G.14, A:G.17, A:T.132, A:S.276 UPG.6: 21 residues within 4Å: Chain A: R.261 Chain B: F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 Ligands: UPG.7, EDO.11 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.232, B:F.266 Hydrogen bonds: B:E.166, B:K.221, B:K.221, B:N.225, B:K.268, B:K.268, B:S.270, B:G.274, B:F.339, B:R.443, B:R.443, A:R.261, A:R.261 Water bridges: B:K.221, B:N.225, B:F.266, B:C.277, B:E.417 Salt bridges: B:K.340, B:K.340 UPG.7: 18 residues within 4Å: Chain B: G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, S.89, V.90, N.91, Y.109, S.131, T.132, S.276, C.277, R.347 Ligands: UPG.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.109 Hydrogen bonds: B:Y.15, B:V.16, B:V.38, B:R.42, B:R.42, B:V.90, B:S.131, B:T.132, B:T.132, B:T.132, B:S.276, B:S.276, B:R.347, B:R.347 Water bridges: B:G.14, B:G.14 UPG.13: 20 residues within 4Å: Chain C: Q.162, F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 Chain D: R.261 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.232, C:F.266 Hydrogen bonds: C:Q.162, C:Q.162, C:E.166, C:K.221, C:K.221, C:N.225, C:K.268, C:K.268, C:S.270, C:G.274, C:F.339, C:R.443, C:R.443, D:R.261, D:R.261 Water bridges: C:F.266, C:C.277, C:C.277, C:E.417 Salt bridges: C:K.340, C:K.340 UPG.14: 17 residues within 4Å: Chain C: I.11, G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, V.90, N.91, S.131, T.132, Q.162, S.276, C.277, R.347 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.11, C:V.38 Hydrogen bonds: C:Y.15, C:V.16, C:R.42, C:R.42, C:V.90, C:S.131, C:T.132, C:T.132, C:Q.162, C:S.276, C:R.347, C:R.347 Water bridges: C:G.14, C:G.17, C:N.39, C:R.116, C:T.132 UPG.18: 21 residues within 4Å: Chain C: R.261 Chain D: Q.162, F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 Ligands: UPG.19 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.232, D:F.266 Hydrogen bonds: D:E.166, D:K.221, D:K.221, D:N.225, D:K.268, D:K.268, D:S.270, D:G.274, D:F.339, D:R.443, D:R.443, C:R.261, C:R.261 Water bridges: D:K.221, D:N.225, D:C.277 Salt bridges: D:K.340, D:K.340 UPG.19: 18 residues within 4Å: Chain D: G.12, G.14, Y.15, V.16, D.37, V.38, R.42, S.89, V.90, N.91, Y.109, S.131, T.132, Q.162, S.276, C.277, R.347 Ligands: UPG.18 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.109 Hydrogen bonds: D:Y.15, D:V.16, D:V.38, D:R.42, D:V.90, D:S.131, D:T.132, D:T.132, D:T.132, D:Q.162, D:S.276, D:S.276, D:R.347, D:R.347 Water bridges: D:G.14, D:G.17, D:K.221 UPG.21: 21 residues within 4Å: Chain E: F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 Chain F: R.261 Ligands: UPG.22, EDO.26 22 PLIP interactions: 20 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:I.232, E:F.266 Hydrogen bonds: E:Q.162, E:E.166, E:K.221, E:K.221, E:N.225, E:K.268, E:K.268, E:S.270, E:G.274, E:F.339, E:R.443, E:R.443, F:R.261, F:R.261 Water bridges: E:L.164, E:S.276, E:C.277, E:E.417 Salt bridges: E:K.340, E:K.340 UPG.22: 17 residues within 4Å: Chain E: G.12, G.14, Y.15, V.16, D.37, V.38, R.42, V.90, N.91, Y.109, S.131, T.132, S.276, C.277, R.347 Ligands: UPG.21, EDO.27 19 PLIP interactions: 19 interactions with chain E Hydrophobic interactions: E:Y.109 Hydrogen bonds: E:Y.15, E:V.16, E:V.38, E:R.42, E:R.42, E:V.90, E:S.131, E:T.132, E:T.132, E:S.276, E:R.347, E:R.347 Water bridges: E:G.14, E:G.17, E:R.42, E:T.132, E:S.276, E:S.276 UPG.29: 20 residues within 4Å: Chain E: R.261 Chain F: Q.162, F.163, L.164, A.165, E.166, K.221, N.225, I.232, F.266, L.267, K.268, S.270, F.273, G.274, C.277, F.278, F.339, K.340, R.443 21 PLIP interactions: 19 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:I.232, F:F.266 Hydrogen bonds: F:Q.162, F:E.166, F:K.221, F:N.225, F:K.268, F:K.268, F:S.270, F:G.274, F:F.339, F:R.443, F:R.443, E:R.261, E:R.261 Water bridges: F:K.221, F:N.225, F:C.277, F:E.417 Salt bridges: F:K.340, F:K.340 UPG.30: 18 residues within 4Å: Chain F: I.11, G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, S.89, V.90, N.91, S.131, T.132, Q.162, S.276, C.277, R.347 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:I.11, F:V.38 Hydrogen bonds: F:Y.15, F:V.16, F:R.42, F:S.131, F:T.132, F:T.132, F:T.132, F:Q.162, F:S.276, F:S.276, F:R.347, F:R.347 Water bridges: F:G.14, F:G.14

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: F.3, E.4, D.84 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: E.290, A.298, R.299, Q.302 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: K.268, A.269, S.270, R.443 Ligands: UPG.1 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: Q.230, Y.300, V.304 Chain B: Q.230, Y.300, V.304 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain B: T.92, A.105, T.132, V.133, P.134, K.280, D.281, N.284 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: E.250, A.253, T.254, N.264, L.267 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain B: F.266 Ligands: UPG.6 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: L.424, Y.426, E.452 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain C: D.329, H.364, H.366 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain C: A.138, R.142, V.157, D.184, T.214 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain C: V.286, E.290, R.299, Q.302 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain E: I.53, Y.54, E.55, P.56, G.57, L.58, K.59, E.60 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain E: H.364, H.366, R.394, L.395, T.397 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain E: K.422, E.423, L.424, Y.426 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain E: A.269, S.270, E.417, R.443 Ligands: UPG.21 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain E: I.11, V.38, A.112, C.113, R.116 Ligands: UPG.22 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain A: Y.97 Chain E: M.359, D.360, G.362, Q.391, R.394, L.395 Ligand excluded by PLIP

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.20: 5 residues within 4Å: Chain C: E.185 Chain D: G.448, H.450, N.451, K.465 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.448, D:H.450, D:N.451, D:K.465 Salt bridges: C:E.185, C:E.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egger, S. et al., Structural and Kinetic Evidence That Catalytic Reaction of Human UDP-glucose 6-Dehydrogenase Involves Covalent Thiohemiacetal and Thioester Enzyme Intermediates. J.Biol.Chem. (2012)

Release Date

2009-11-17

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