SMTL ID : 2wdz.1 (1 other biounit)

CRYSTAL STRUCTURE OF THE SHORT CHAIN DEHYDROGENASE GALACTITOL-DEHYDROGENASE (GATDH) OF RHODOBACTER SPHAEROIDES IN COMPLEX WITH NAD+ AND 1,2-PENTANDIOL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: W.254 Chain C: W.254 Ligands: MG.8 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: W.254 Chain D: W.254 Ligands: MG.12 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: W.254 Chain C: W.254 Ligands: MG.1 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: W.254 Chain D: W.254 Ligands: MG.5 No protein-ligand interaction detected (PLIP)

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

NAD.2: 29 residues within 4Å: Chain A: G.18, G.20, S.21, G.22, I.23, G.24, D.42, R.43, 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: 1SP.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.189 Hydrogen bonds: A:G.20, A:S.21, A:S.21, A:S.21, A:I.23, A:G.24, A:R.43, A:D.66, A:V.67, A:S.92, A:G.94, A:K.163, A:V.192, A:V.192, A:T.194, A:T.194, A:E.195, A:M.196 Water bridges: A:G.22 NAD.6: 30 residues within 4Å: Chain B: G.18, G.20, 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, Y.191, V.192, T.194, E.195, M.196, T.197 Ligands: 1SP.7 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.189 Hydrogen bonds: B:G.18, B:G.20, B:I.23, B:R.43, B:R.43, B:D.66, B:D.66, B:V.67, B:A.93, B:G.94, B:Y.159, B:K.163, B:V.192, B:V.192, B:T.194, B:E.195, B:M.196 Water bridges: B:G.24 NAD.9: 29 residues within 4Å: Chain C: G.18, G.20, S.21, G.22, I.23, G.24, D.42, R.43, 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: 1SP.10 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:P.189 Hydrogen bonds: C:G.20, C:S.21, C:S.21, C:S.21, C:I.23, C:G.24, C:R.43, C:D.66, C:D.66, C:V.67, C:S.92, C:G.94, C:Y.159, C:K.163, C:V.192, C:V.192, C:T.194, C:E.195, C:M.196 Water bridges: C:G.22 NAD.13: 30 residues within 4Å: Chain D: G.18, G.20, 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, Y.191, V.192, T.194, E.195, M.196, T.197 Ligands: 1SP.14 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:P.189 Hydrogen bonds: D:G.18, D:G.20, D:I.23, D:R.43, D:R.43, D:D.66, D:V.67, D:A.93, D:G.94, D:K.163, D:V.192, D:V.192, D:T.194, D:T.194, D:E.195, D:M.196 Water bridges: D:G.24

6 x 1SP: (2S)-PENTANE-1,2-DIOL

1SP.3: 9 residues within 4Å: Chain A: A.96, S.144, S.146, N.151, Q.154, Y.159, Y.191, T.197 Ligands: NAD.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.96, A:Y.159 Hydrogen bonds: A:S.144, A:Y.159 1SP.4: 5 residues within 4Å: Chain A: A.45, L.48, D.49, R.62, V.64 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.48, A:D.49 1SP.7: 9 residues within 4Å: Chain B: S.144, M.145, S.146, N.151, Q.154, Y.159, Y.191, T.197 Ligands: NAD.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.144, B:S.144, B:N.151 1SP.10: 9 residues within 4Å: Chain C: A.96, S.144, S.146, N.151, Q.154, Y.159, Y.191, T.197 Ligands: NAD.9 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.96, C:Y.159 Hydrogen bonds: C:S.144 1SP.11: 5 residues within 4Å: Chain C: A.45, L.48, D.49, R.62, V.64 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.48, C:D.49 1SP.14: 9 residues within 4Å: Chain D: S.144, M.145, S.146, N.151, Q.154, Y.159, Y.191, T.197 Ligands: NAD.13 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.144, D:S.144, D:N.151

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

2010-03-31

Peptides

SHORT-CHAIN DEHYDROGENASE/REDUCTASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

SHORT-CHAIN DEHYDROGENASE/REDUCTASE

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