SMTL ID : 6iuy.1

Structure of DsGPDH of Dunaliella salina

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: S.264, G.265, A.266, W.267, A.268, W.297, H.299, E.301, Y.321, C.350, A.351, P.352, H.353, F.355, I.359, L.378, T.379, K.380, N.411, I.412, A.413, R.528, G.559, Q.560, K.561, Q.563 Ligands: 13P.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:W.267 Hydrogen bonds: A:S.264, A:S.264, A:G.265, A:G.265, A:A.266, A:W.267, A:A.268, A:H.299, A:K.380, A:K.380, A:A.413, A:K.561, A:Q.563 Water bridges: A:S.264, A:H.299, A:R.528, A:R.528, A:R.528, A:R.528, A:R.528 Salt bridges: A:R.528, A:R.528 pi-Stacking: A:W.267, A:H.299, A:F.355 NAD.5: 26 residues within 4Å: Chain B: S.264, G.265, A.266, W.267, A.268, W.297, H.299, E.301, Y.321, C.350, A.351, P.352, F.355, L.378, T.379, K.380, N.411, I.412, A.413, N.465, R.528, G.559, Q.560, K.561, Q.563 Ligands: 13P.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:W.267 Hydrogen bonds: B:S.264, B:G.265, B:A.266, B:W.267, B:A.268, B:H.299, B:K.380, B:A.413, B:N.465, B:Q.560, B:K.561 Water bridges: B:S.264, B:S.264, B:S.264, B:S.264, B:S.264, B:R.528, B:R.528 Salt bridges: B:R.528, B:R.528 pi-Stacking: B:W.267, B:H.299, B:F.355 pi-Cation interactions: B:H.299, B:K.464

2 x 13P: 1,3-DIHYDROXYACETONEPHOSPHATE(Non-covalent)

13P.2: 9 residues within 4Å: Chain A: K.380, K.464, N.465, S.523, G.527, R.528, N.529, Q.563 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.380, A:K.464, A:R.528, A:R.528, A:N.529, A:N.529 Water bridges: A:G.527 Salt bridges: A:K.464, A:R.528 13P.6: 9 residues within 4Å: Chain B: K.380, I.412, K.464, N.465, S.523, G.527, R.528, N.529 Ligands: NAD.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.464, B:N.465, B:R.528, B:R.528, B:N.529 Salt bridges: B:R.528

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: D.41, D.43, R.44, G.133, K.185, S.209, R.233 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.44, A:G.133, A:K.185, A:K.185, A:S.209, A:R.233, A:R.233

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.41, D.43, D.206 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.41, A:D.43, A:D.206 MG.7: 4 residues within 4Å: Chain B: D.41, D.43, R.44, D.206 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.41, B:D.43, B:D.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Q. et al., The unusual di-domain structure of Dunaliella salina glycerol-3-phosphate dehydrogenase enables direct conversion of dihydroxyacetone phosphate to glycerol. Plant J. (2020)

Release Date

2019-12-04

Peptides

Glycerol-3-phosphate dehydrogenase [NAD(+)]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycerol-3-phosphate dehydrogenase [NAD(+)]