SMTL ID : 7wwx.1

Crystal structure of Herbaspirillum huttiense L-arabinose 1-dehydrogenase (NAD bound form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: G.36, T.39, G.40, I.41, D.60, I.61, C.86, D.87, L.88, N.114, A.115, A.116, I.137, F.164, S.165, S.166, Y.179, K.183, P.209, G.210, W.211, V.212, T.214, R.216, Q.217 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.209 Hydrogen bonds: A:T.39, A:T.39, A:I.41, A:I.61, A:D.87, A:L.88, A:N.114, A:V.212, A:V.212, A:Q.217 Water bridges: A:G.42, A:N.117, A:K.183, A:T.214, A:Q.217 Salt bridges: A:R.216 NAD.3: 25 residues within 4Å: Chain B: G.36, T.39, G.40, I.41, D.60, I.61, C.86, D.87, L.88, N.114, A.115, A.116, I.137, F.164, S.165, S.166, Y.179, K.183, P.209, G.210, W.211, V.212, T.214, R.216, Q.217 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:P.209 Hydrogen bonds: B:T.39, B:T.39, B:I.41, B:I.61, B:D.87, B:L.88, B:N.114, B:V.212, B:V.212 Water bridges: B:G.42, B:N.117, B:K.183, B:R.216, B:Q.217, B:Q.217 Salt bridges: B:R.216 NAD.4: 25 residues within 4Å: Chain C: G.36, T.39, G.40, I.41, D.60, I.61, C.86, D.87, L.88, N.114, A.115, A.116, I.137, F.164, S.165, S.166, Y.179, K.183, P.209, G.210, W.211, V.212, T.214, R.216, Q.217 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.209 Hydrogen bonds: C:T.39, C:T.39, C:T.39, C:I.41, C:I.61, C:D.87, C:D.87, C:L.88, C:N.114, C:Y.179, C:V.212, C:V.212, C:Q.217 Water bridges: C:G.42, C:N.117, C:K.183, C:T.214, C:Q.217 Salt bridges: C:R.216 NAD.6: 25 residues within 4Å: Chain D: G.36, T.39, G.40, I.41, D.60, I.61, C.86, D.87, L.88, N.114, A.115, A.116, I.137, F.164, S.165, S.166, Y.179, K.183, P.209, G.210, W.211, V.212, T.214, R.216, Q.217 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.209 Hydrogen bonds: D:T.39, D:T.39, D:T.39, D:I.41, D:I.61, D:D.87, D:D.87, D:L.88, D:N.114, D:Y.179, D:V.212, D:V.212 Water bridges: D:G.42, D:N.117, D:K.183, D:R.216, D:Q.217, D:Q.217 Salt bridges: D:R.216

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: Q.104, L.105, G.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.31 PEG.5: 3 residues within 4Å: Chain C: Q.104, L.105, G.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, S. et al., Crystal structure of L-arabinose 1-dehydrogenase as a short-chain reductase/dehydrogenase protein. Biochem.Biophys.Res.Commun. (2022)

Release Date

2022-03-30

Peptides

NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)