SMTL ID : 7q53.1

Single Particle Cryo-EM structure of photosynthetic A2B2 glyceraldehyde 3-phosphate dehydrogenase from Spinacia oleracia

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: G.8, G.10, R.11, I.12, N.34, D.35, N.79, R.80, G.98, T.99, G.100, V.101, T.122, A.123, S.154, T.185, N.319, E.320, Y.323 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.323 Hydrogen bonds: A:R.11, A:I.12, A:N.34, A:R.80, A:R.80, A:T.99 pi-Cation interactions: A:R.80 NAD.2: 23 residues within 4Å: Chain B: G.8, G.10, R.11, I.12, R.14, N.34, D.35, T.36, D.79, R.80, G.98, T.99, G.100, V.101, T.122, A.123, S.152, C.153, T.183, N.316, E.317, Y.320 Chain C: S.194 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.320 Hydrogen bonds: B:R.11, B:I.12, B:R.14, B:N.34, B:T.36, B:R.80, B:T.122, C:S.194 pi-Cation interactions: B:R.80, B:R.80 NAD.3: 20 residues within 4Å: Chain C: G.8, G.10, R.11, I.12, N.34, D.35, N.79, R.80, G.98, T.99, G.100, V.101, T.122, A.123, S.154, C.155, T.185, N.319, E.320, Y.323 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.323 Hydrogen bonds: C:R.11, C:I.12, C:N.34, C:R.80, C:R.80, C:T.99, C:E.320 pi-Cation interactions: C:R.80 NAD.4: 23 residues within 4Å: Chain A: S.194 Chain D: G.8, G.10, R.11, I.12, R.14, N.34, D.35, T.36, D.79, R.80, G.98, T.99, G.100, V.101, T.122, A.123, S.152, C.153, T.183, N.316, E.317, Y.320 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Y.320 Hydrogen bonds: D:R.11, D:I.12, D:R.14, D:N.34, D:T.36, D:T.36, D:R.80, D:G.98, D:T.183, D:T.183, D:E.317 pi-Cation interactions: D:R.80, D:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marotta, R. et al., Unravelling the regulation pathway of photosynthetic AB-GAPDH. Acta Crystallogr D Struct Biol (2022)

Release Date

2022-11-16

Peptides

Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic: AC
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

C
Q

B
P

D
R

Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

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