SMTL ID : 3lqf.1

Crystal structure of the short-chain dehydrogenase Galactitol-Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD and erythritol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: W.254 Chain B: W.254 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain C: W.254 Chain D: W.254 No protein-ligand interaction detected (PLIP)

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

NAD.2: 30 residues within 4Å: Chain A: G.18, G.20, S.21, G.22, I.23, G.24, D.42, R.43, E.44, A.65, D.66, V.67, S.92, A.93, G.94, V.115, L.142, G.143, S.144, Y.159, K.163, P.189, G.190, Y.191, V.192, T.194, E.195, M.196, T.197 Ligands: MRY.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.189 Hydrogen bonds: A:G.18, A:G.20, A:I.23, A:G.24, A:R.43, A:E.44, A:D.66, A:V.67, A:S.92, A:G.94, A:Y.159, A:K.163, A:V.192, A:V.192, A:T.194, A:E.195, A:M.196 NAD.4: 27 residues within 4Å: Chain B: S.21, G.22, I.23, G.24, D.42, R.43, E.44, A.65, D.66, V.67, S.92, A.93, G.94, I.95, L.142, G.143, S.144, Y.159, K.163, P.189, G.190, Y.191, V.192, T.194, M.196, T.197 Ligands: MRY.5 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:I.23, B:G.24, B:R.43, B:R.43, B:E.44, B:D.66, B:V.67, B:S.92, B:K.163, B:V.192, B:V.192, B:T.194 Water bridges: B:G.18, B:S.21, B:G.94 pi-Cation interactions: B:R.43 NAD.6: 27 residues within 4Å: Chain C: G.18, S.21, G.22, I.23, D.42, R.43, E.44, A.65, D.66, V.67, S.92, A.93, G.94, I.95, V.115, L.142, G.143, S.144, Y.159, K.163, P.189, G.190, V.192, T.194, M.196, T.197 Ligands: MRY.7 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:P.189 Hydrogen bonds: C:G.18, C:G.20, C:I.23, C:R.43, C:D.66, C:V.67, C:S.92, C:G.94, C:K.163, C:V.192, C:T.194, C:T.194, C:M.196, C:T.197, C:T.197 Water bridges: C:G.24, C:E.195 NAD.9: 28 residues within 4Å: Chain D: G.18, S.21, G.22, I.23, G.24, D.42, R.43, A.65, D.66, V.67, S.92, A.93, G.94, I.95, V.115, L.142, G.143, S.144, Y.159, K.163, P.189, G.190, Y.191, V.192, T.194, M.196, T.197 Ligands: MRY.10 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.21, D:S.21, D:I.23, D:G.24, D:R.43, D:R.43, D:D.66, D:D.66, D:V.67, D:S.92, D:G.94, D:Y.159, D:K.163, D:V.192, D:V.192, D:T.194, D:T.194

4 x MRY: MESO-ERYTHRITOL(Non-covalent)

MRY.3: 9 residues within 4Å: Chain A: A.96, N.151, Q.154, Y.159, Y.191, M.196, T.197, M.200 Ligands: NAD.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.159 Water bridges: A:S.144 MRY.5: 8 residues within 4Å: Chain B: A.96, L.98, N.151, Q.154, A.156, Y.159, Y.191 Ligands: NAD.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.154 Water bridges: B:A.96 MRY.7: 11 residues within 4Å: Chain C: L.98, N.151, Q.154, A.156, Y.159, Y.191, M.196, T.197, M.200, W.210 Ligands: NAD.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.154, C:T.197 Water bridges: C:S.144, C:N.151, C:Y.159 MRY.10: 6 residues within 4Å: Chain D: A.96, N.151, Q.154, Y.159, M.196 Ligands: NAD.9 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.159 Water bridges: D:S.144, D:S.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carius, Y. et al., Structural insight into substrate differentiation of the sugar-metabolizing enzyme galactitol dehydrogenase from Rhodobacter sphaeroides D. J.Biol.Chem. (2010)

Release Date

2010-04-21

Peptides

Galactitol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Galactitol dehydrogenase

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