SMTL ID : 2qg4.3 (5 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 14 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 11 PLIP interactions: 11 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:G.17, A:R.42, A:R.42, A:A.112 Salt bridges: A:R.42 NAD.5: 26 residues within 4Å: Chain B: I.11, G.12, 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.6 29 PLIP interactions: 29 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:N.91, 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:T.132, B:R.347, B:R.347, B:R.347 Salt bridges: B:R.42, B:R.347, B:R.347

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

UGA.2: 21 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, D.281, F.339, K.340, R.443 Chain B: R.261 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.232 Hydrogen bonds: 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, B:R.261, B:R.261 Water bridges: A:E.162, A:E.162 Salt bridges: A:K.221, A:K.340, A:K.340 pi-Stacking: A:F.266 UGA.6: 21 residues within 4Å: Chain A: R.261 Chain B: 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 Ligands: NAD.5 28 PLIP interactions: 26 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:F.339, B:R.443, B:R.443, A:R.261, A:R.261 Water bridges: B:F.163, B:A.165, B:F.266, B:S.276, B:S.276, B:C.277, B:K.340, B:K.340, B:K.340 Salt bridges: B:K.221, B:K.340, B:K.340

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

CL.3: 3 residues within 4Å: Chain B: W.418, D.419, M.420 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: D.184, T.214, W.215 Ligand excluded by PLIP

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

EDO.7: 8 residues within 4Å: Chain A: Q.230, Y.300, Q.303, V.304 Chain B: Q.230, Y.300, Q.303, V.304 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.230

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

UDP-glucose 6-dehydrogenase

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