SMTL ID : 7q54.1

Single Particle Cryo-EM structure of photosynthetic A4B4-glyceraldehyde 3-phosphate dehydrogenase from Spinacia oleracia.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: N.90, G.91, F.92, G.93, R.94, I.95, N.117, N.162, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, H.265, G.269, N.402, E.403, Y.406 Chain D: L.254 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.406 Hydrogen bonds: A:N.90, A:F.92, A:R.94, A:R.94, A:I.95, A:G.96, A:R.97, A:R.163, A:R.163, A:G.181, A:T.182 Salt bridges: A:R.94, A:R.94 pi-Cation interactions: A:R.163 NAD.2: 30 residues within 4Å: Chain B: N.72, G.73, G.75, R.76, I.77, G.78, N.99, D.100, T.101, D.144, R.145, E.162, G.163, T.164, G.165, F.167, V.168, T.187, A.188, S.217, C.218, H.245, T.248, D.250, R.299, N.381, E.382, Y.385 Chain G: E.445, E.446 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:N.72, B:G.73, B:G.75, B:G.75, B:R.76, B:I.77, B:G.78, B:N.99, B:T.101, B:T.101, B:R.145, B:R.145, B:T.164, B:T.187, B:T.248, B:D.250, B:R.299, B:E.382, G:E.445 pi-Stacking: B:Y.385 pi-Cation interactions: B:R.145 NAD.3: 25 residues within 4Å: Chain B: S.257 Chain C: N.90, G.91, F.92, G.93, R.94, I.95, N.98, N.117, D.118, R.163, E.180, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, E.403, Y.406 Chain G: Y.450, E.451 19 PLIP interactions: 3 interactions with chain G, 16 interactions with chain C Hydrophobic interactions: G:E.451, C:T.268, C:E.403, C:Y.406 Hydrogen bonds: G:Y.450, G:E.451, C:F.92, C:F.92, C:R.94, C:R.94, C:I.95, C:G.96, C:N.98, C:R.163, C:R.163, C:R.163, C:E.180 pi-Cation interactions: C:R.163, C:R.163 NAD.4: 29 residues within 4Å: Chain A: A.276 Chain D: N.72, G.73, G.75, R.76, I.77, G.78, N.99, D.100, T.101, D.144, R.145, E.162, G.163, T.164, G.165, F.167, V.168, T.187, A.188, S.217, C.218, H.245, T.248, D.250, R.299, N.381, E.382, Y.385 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:N.72, D:G.73, D:G.75, D:G.75, D:R.76, D:I.77, D:G.78, D:N.99, D:T.101, D:R.145, D:R.145, D:G.163, D:T.187, D:D.250, D:R.299 pi-Stacking: D:Y.385 pi-Cation interactions: D:R.145 NAD.5: 20 residues within 4Å: Chain E: N.90, G.91, G.93, R.94, I.95, G.96, N.98, N.117, N.162, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, S.237, G.269, Y.406 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:Y.406, E:Y.406 Hydrogen bonds: E:N.90, E:R.94, E:I.95, E:G.96, E:N.98, E:N.117, E:R.163, E:G.181, E:T.182, E:T.205, E:G.269 NAD.6: 29 residues within 4Å: Chain C: E.445 Chain F: N.72, G.73, G.75, R.76, I.77, G.78, N.99, D.100, T.101, D.144, R.145, E.162, G.163, T.164, G.165, F.167, V.168, T.187, A.188, S.217, C.218, H.245, T.248, D.250, R.299, N.381, E.382, Y.385 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:N.72, F:G.73, F:G.75, F:G.75, F:R.76, F:I.77, F:G.78, F:N.99, F:T.101, F:R.145, F:R.145, F:T.164, F:T.187, F:D.250, F:R.299 pi-Stacking: F:Y.385 pi-Cation interactions: F:R.145 NAD.7: 26 residues within 4Å: Chain C: Y.450, E.451 Chain F: L.254, S.257 Chain G: G.91, F.92, G.93, R.94, I.95, G.96, N.117, D.118, S.119, N.162, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, G.269, D.270, E.403, Y.406 17 PLIP interactions: 16 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:A.206, G:Y.406, C:E.451 Hydrogen bonds: G:G.93, G:R.94, G:I.95, G:G.96, G:N.117, G:D.118, G:R.163, G:R.163, G:R.163, G:G.269, G:D.270, G:E.403 pi-Cation interactions: G:R.163, G:R.163 NAD.8: 30 residues within 4Å: Chain E: R.272, A.276 Chain H: N.72, G.73, G.75, R.76, I.77, G.78, N.99, D.100, T.101, D.144, R.145, E.162, G.163, T.164, G.165, F.167, V.168, T.187, A.188, S.217, C.218, H.245, T.248, D.250, R.299, N.381, E.382, Y.385 21 PLIP interactions: 20 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:N.72, H:G.73, H:G.75, H:G.75, H:R.76, H:I.77, H:G.78, H:N.99, H:T.101, H:T.101, H:R.145, H:R.145, H:G.163, H:T.187, H:T.248, H:D.250, H:R.299, H:E.382, E:R.272 pi-Stacking: H:Y.385 pi-Cation interactions: H:R.145

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: ACEG
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

C
O

E
A

G
C

B
R

D
P

F
B

H
D

Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

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