SMTL ID : 2qg4.4 (5 other biounits)

Crystal structure of human UDP-glucose dehydrogenase product complex with UDP-glucuronate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 15 residues within 4Å: Chain A: I.11, G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, I.76, S.89, V.90, N.91, Y.109, C.113 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.15, A:V.16, A:V.38, A:R.42, A:R.42 Water bridges: A:G.14, A:R.42, A:V.90, A:T.92, A:A.112, A:R.116, A:T.132 Salt bridges: A:R.42 NAD.6: 27 residues within 4Å: Chain B: I.11, G.12, A.13, G.14, Y.15, V.16, D.37, V.38, R.42, I.76, S.89, V.90, N.91, T.92, Y.109, A.112, S.131, T.132, E.162, L.164, E.166, K.221, S.276, C.277, K.280, R.347 Ligands: UGA.7 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:V.16, B:E.162 Hydrogen bonds: B:Y.15, B:V.16, B:V.38, B:R.42, B:R.42, B:V.90, B:T.92, B:Y.109, B:T.132, B:E.166, B:E.166, B:S.276, B:K.280, B:K.280, B:R.347 Water bridges: B:G.14, B:G.17, B:R.42, B:R.42, B:R.116, B:R.116, B:E.166, B:R.347, B:R.347, B:R.347, B:R.347 Salt bridges: B:R.42, B:R.347, B:R.347 NAD.8: 15 residues within 4Å: Chain C: I.11, G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, I.76, S.89, V.90, N.91, Y.109, C.113 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.15, C:V.16, C:V.38, C:R.42, C:R.42 Water bridges: C:G.14, C:R.42, C:V.90, C:T.92, C:A.112, C:R.116, C:T.132 Salt bridges: C:R.42 NAD.13: 27 residues within 4Å: Chain D: I.11, G.12, A.13, G.14, Y.15, V.16, D.37, V.38, R.42, I.76, S.89, V.90, N.91, T.92, Y.109, A.112, S.131, T.132, E.162, L.164, E.166, K.221, S.276, C.277, K.280, R.347 Ligands: UGA.14 31 PLIP interactions: 31 interactions with chain D Hydrophobic interactions: D:V.16, D:E.162 Hydrogen bonds: D:Y.15, D:V.16, D:V.38, D:R.42, D:R.42, D:V.90, D:T.92, D:Y.109, D:T.132, D:E.166, D:E.166, D:S.276, D:K.280, D:K.280, D:R.347 Water bridges: D:G.14, D:G.17, D:R.42, D:R.42, D:R.116, D:R.116, D:E.166, D:R.347, D:R.347, D:R.347, D:R.347 Salt bridges: D:R.42, D:R.347, D:R.347 NAD.15: 15 residues within 4Å: Chain E: I.11, G.12, G.14, Y.15, V.16, D.37, V.38, N.39, R.42, I.76, S.89, V.90, N.91, Y.109, C.113 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:Y.15, E:V.16, E:V.38, E:R.42, E:R.42 Water bridges: E:G.14, E:R.42, E:V.90, E:T.92, E:A.112, E:R.116, E:T.132 Salt bridges: E:R.42 NAD.20: 27 residues within 4Å: Chain F: I.11, G.12, A.13, G.14, Y.15, V.16, D.37, V.38, R.42, I.76, S.89, V.90, N.91, T.92, Y.109, A.112, S.131, T.132, E.162, L.164, E.166, K.221, S.276, C.277, K.280, R.347 Ligands: UGA.21 31 PLIP interactions: 31 interactions with chain F Hydrophobic interactions: F:V.16, F:E.162 Hydrogen bonds: F:Y.15, F:V.16, F:V.38, F:R.42, F:R.42, F:V.90, F:T.92, F:Y.109, F:T.132, F:E.166, F:E.166, F:S.276, F:K.280, F:K.280, F:R.347 Water bridges: F:G.14, F:G.17, F:R.42, F:R.42, F:R.116, F:R.116, F:E.166, F:R.347, F:R.347, F:R.347, F:R.347 Salt bridges: F:R.42, F:R.347, F:R.347

6 x UGA: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID(Non-covalent)

UGA.2: 20 residues within 4Å: Chain A: E.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 B: R.261 21 PLIP interactions: 2 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:R.261, B:R.261, A:F.163, A:L.164, A:E.166, A:K.221, A:N.225, A:K.268, A:K.268, A:S.270, A:G.274, A:G.274, A:F.339, A:R.443, A:R.443 Hydrophobic interactions: A:I.232, A:F.266 Water bridges: A:F.266 Salt bridges: A:K.221, A:K.340, A:K.340 UGA.7: 22 residues within 4Å: Chain A: R.261 Chain B: E.162, F.163, L.164, A.165, E.166, K.221, N.225, L.228, 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: NAD.6 27 PLIP interactions: 25 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.232, B:F.266 Hydrogen bonds: B:F.163, B:E.166, B:K.221, B:N.225, B:K.268, B:K.268, B:S.270, B:G.274, B:G.274, B:D.281, B:F.339, B:R.443, B:R.443, A:R.261, A:R.261 Water bridges: B:F.266, B:S.276, B:C.277, B:C.277, B:K.340, B:K.340, B:K.340 Salt bridges: B:K.221, B:K.340, B:K.340 UGA.9: 20 residues within 4Å: Chain C: E.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 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.232, C:F.266 Hydrogen bonds: C:F.163, C:L.164, C:E.166, C:K.221, C:N.225, C:K.268, C:K.268, C:S.270, C:G.274, C:G.274, C:F.339, C:R.443, C:R.443, D:R.261, D:R.261 Water bridges: C:F.266 Salt bridges: C:K.221, C:K.340, C:K.340 UGA.14: 22 residues within 4Å: Chain C: R.261 Chain D: E.162, F.163, L.164, A.165, E.166, K.221, N.225, L.228, 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: NAD.13 27 PLIP interactions: 25 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.232, D:F.266 Hydrogen bonds: D:F.163, D:E.166, D:K.221, D:N.225, D:K.268, D:K.268, D:S.270, D:G.274, D:G.274, D:D.281, D:F.339, D:R.443, D:R.443, C:R.261, C:R.261 Water bridges: D:F.266, D:S.276, D:C.277, D:C.277, D:K.340, D:K.340, D:K.340 Salt bridges: D:K.221, D:K.340, D:K.340 UGA.16: 20 residues within 4Å: Chain E: E.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 F: R.261 21 PLIP interactions: 19 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:I.232, E:F.266 Hydrogen bonds: E:F.163, E:L.164, E:E.166, E:K.221, E:N.225, E:K.268, E:K.268, E:S.270, E:G.274, E:G.274, E:F.339, E:R.443, E:R.443, F:R.261, F:R.261 Water bridges: E:F.266 Salt bridges: E:K.221, E:K.340, E:K.340 UGA.21: 22 residues within 4Å: Chain E: R.261 Chain F: E.162, F.163, L.164, A.165, E.166, K.221, N.225, L.228, 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: NAD.20 27 PLIP interactions: 25 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:I.232, F:F.266 Hydrogen bonds: F:F.163, F:E.166, F:K.221, F:N.225, F:K.268, F:K.268, F:S.270, F:G.274, F:G.274, F:D.281, F:F.339, F:R.443, F:R.443, E:R.261, E:R.261 Water bridges: F:F.266, F:S.276, F:C.277, F:C.277, F:K.340, F:K.340, F:K.340 Salt bridges: F:K.221, F:K.340, F:K.340

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

EDO.3: 8 residues within 4Å: Chain A: Q.230, Y.300, Q.303, V.304 Chain B: Q.230, Y.300, Q.303, V.304 No protein-ligand interaction detected (PLIP) EDO.10: 8 residues within 4Å: Chain C: Q.230, Y.300, Q.303, V.304 Chain D: Q.230, Y.300, Q.303, V.304 No protein-ligand interaction detected (PLIP) EDO.17: 8 residues within 4Å: Chain E: Q.230, Y.300, Q.303, V.304 Chain F: Q.230, Y.300, Q.303, V.304 No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain B: W.418, D.419, M.420 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: G.183, D.184, T.214, W.215 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain D: W.418, D.419, M.420 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain D: G.183, D.184, T.214, W.215 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain F: W.418, D.419, M.420 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain F: G.183, D.184, T.214, W.215 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egger, S. et al., Structure and mechanism of human UDP-glucose 6-dehydrogenase. J.Biol.Chem. (2011)

Release Date

2007-07-10

Peptides

UDP-glucose 6-dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
G

D
H

E
G

F
H

UDP-glucose 6-dehydrogenase

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