SMTL ID : 7q55.1

Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracia.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-mer

Ligands

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

NAD.1: 20 residues within 4Å: Chain A: G.91, F.92, G.93, R.94, I.95, R.97, N.117, S.119, N.162, R.163, G.181, T.182, T.205, C.238, D.270, N.402, E.403, Y.406 Chain G: A.443, E.451 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:N.402, A:Y.406 Hydrogen bonds: A:F.92, A:F.92, A:R.94, A:R.94, A:I.95, A:R.97, A:R.97, A:N.117, A:S.119, A:R.163, A:R.163, A:R.163, A:T.205 pi-Cation interactions: A:R.163, A:R.163 NAD.2: 23 residues within 4Å: Chain B: N.72, G.73, F.74, G.75, R.76, I.77, N.99, D.100, T.101, D.144, R.145, E.162, G.163, T.164, G.165, V.166, T.187, A.188, S.217, C.218, N.381, Y.385 Chain C: S.277 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.385 Hydrogen bonds: B:N.72, B:R.76, B:T.101, B:E.162, B:T.164, B:T.187, B:N.381, C:S.277, C:S.277 Salt bridges: B:R.76 NAD.3: 19 residues within 4Å: Chain C: F.92, G.93, R.94, I.95, R.97, S.119, R.163, G.181, T.182, G.183, T.205, S.237, C.238, D.270, N.402, E.403, Y.406 Chain M: A.443, E.451 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.406, C:Y.406 Hydrogen bonds: C:F.92, C:F.92, C:G.93, C:R.94, C:I.95, C:R.97, C:S.119, C:R.163, C:R.163, C:D.270, C:E.403 NAD.4: 26 residues within 4Å: Chain D: N.72, G.73, F.74, G.75, R.76, I.77, R.79, N.99, D.100, T.101, D.144, R.145, E.162, G.163, T.164, G.165, T.187, A.188, S.217, C.218, T.219, H.245, G.249, R.299, N.381, Y.385 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.73, D:G.75, D:R.76, D:I.77, D:R.79, D:T.101, D:G.163, D:G.165, D:A.188, D:C.218, D:T.219, D:G.249, D:N.381 NAD.5: 20 residues within 4Å: Chain E: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, S.119, N.162, R.163, G.181, T.182, T.205, S.237, C.238, N.402, E.403, Y.406 Chain K: E.451 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:Y.406, E:Y.406 Hydrogen bonds: E:F.92, E:F.92, E:G.93, E:R.94, E:I.95, E:S.119, E:G.181, E:T.205 NAD.6: 18 residues within 4Å: Chain F: G.75, R.76, I.77, D.100, T.101, R.145, G.163, T.164, F.167, T.187, S.217, C.218, T.219, H.245, R.299, E.382, Y.385 Chain G: A.276 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.75, F:R.76, F:I.77, F:T.101, F:R.145, F:G.163, F:C.218 Salt bridges: F:R.76, F:R.76 pi-Cation interactions: F:R.145 NAD.7: 21 residues within 4Å: Chain A: A.443, E.451 Chain G: N.90, F.92, G.93, R.94, I.95, N.117, D.118, N.162, R.163, E.180, G.181, T.182, G.183, T.205, A.206, C.238, N.402, E.403, Y.406 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: G:Y.406, G:Y.406, A:E.451 Hydrogen bonds: G:R.94, G:I.95, G:R.163, G:R.163, G:R.163, G:E.403, G:E.403, A:E.451 pi-Cation interactions: G:R.163, G:R.163 NAD.8: 21 residues within 4Å: Chain H: N.72, G.73, F.74, G.75, R.76, I.77, D.100, T.101, D.144, R.145, G.163, T.164, V.166, F.167, T.187, S.217, C.218, H.245, N.381, E.382, Y.385 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:F.74, H:R.76, H:I.77, H:T.101, H:G.163, H:T.187, H:E.382, H:E.382 Salt bridges: H:R.76, H:R.76 pi-Stacking: H:Y.385 pi-Cation interactions: H:R.145 NAD.9: 17 residues within 4Å: Chain I: G.91, F.92, G.93, R.94, I.95, R.97, N.117, S.119, N.162, R.163, G.181, T.182, G.183, T.205, N.402, Y.406 Chain O: E.451 18 PLIP interactions: 17 interactions with chain I, 1 interactions with chain O Hydrophobic interactions: I:I.95, I:N.402 Hydrogen bonds: I:F.92, I:F.92, I:F.92, I:R.94, I:I.95, I:R.97, I:S.119, I:R.163, I:R.163, I:R.163, I:N.402, O:E.451 Salt bridges: I:R.97 pi-Stacking: I:Y.406 pi-Cation interactions: I:R.163, I:R.163 NAD.10: 19 residues within 4Å: Chain J: G.73, F.74, G.75, R.76, I.77, D.100, T.101, D.144, R.145, G.163, T.164, G.165, T.187, A.188, S.217, C.218, E.382, Y.385 Chain K: A.276 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:A.188, J:Y.385 Hydrogen bonds: J:F.74, J:G.75, J:R.76, J:I.77, J:T.101, J:T.101, J:R.145, J:R.145, J:C.218 Salt bridges: J:R.76 NAD.11: 17 residues within 4Å: Chain E: A.443, E.451 Chain K: F.92, G.93, R.94, I.95, R.97, R.163, G.181, T.182, G.183, V.184, T.205, C.238, N.402, E.403, Y.406 12 PLIP interactions: 12 interactions with chain K Hydrophobic interactions: K:Y.406 Hydrogen bonds: K:F.92, K:G.93, K:R.94, K:I.95, K:G.96, K:R.97, K:R.163, K:T.182, K:E.403, K:E.403 Salt bridges: K:R.97 NAD.12: 23 residues within 4Å: Chain L: N.72, G.73, F.74, G.75, R.76, I.77, R.79, D.100, T.101, D.144, R.145, G.163, T.164, G.165, T.187, A.188, S.217, C.218, T.219, H.245, R.299, N.381, Y.385 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:G.73, L:G.75, L:R.76, L:I.77, L:R.79, L:T.101, L:T.101, L:G.163, L:C.218, L:N.381 Salt bridges: L:R.76, L:R.76 NAD.13: 21 residues within 4Å: Chain M: N.90, G.91, F.92, G.93, R.94, I.95, S.119, N.162, R.163, E.180, G.181, T.182, G.183, F.185, T.205, S.237, C.238, N.402, E.403, Y.406 Chain P: A.256 13 PLIP interactions: 13 interactions with chain M Hydrophobic interactions: M:Y.406, M:Y.406 Hydrogen bonds: M:N.90, M:F.92, M:R.94, M:I.95, M:S.119, M:R.163, M:R.163, M:T.182, M:T.182 pi-Cation interactions: M:R.163, M:R.163 NAD.14: 21 residues within 4Å: Chain N: N.72, G.73, F.74, G.75, R.76, I.77, D.100, T.101, D.144, R.145, G.163, T.164, G.165, T.187, A.188, S.217, C.218, T.219, R.299, E.382, Y.385 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:F.74, N:R.76, N:I.77, N:R.79, N:T.101, N:R.145, N:R.145, N:G.163, N:T.187, N:A.188, N:C.218, N:T.219 NAD.15: 22 residues within 4Å: Chain I: Y.450, E.451 Chain O: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, N.162, R.163, G.181, T.182, G.183, T.205, A.206, P.207, C.238, H.265, N.402, E.403 12 PLIP interactions: 10 interactions with chain O, 2 interactions with chain I Hydrogen bonds: O:F.92, O:G.93, O:R.94, O:I.95, O:R.163, O:R.163, O:T.182, O:N.402, I:Y.450 pi-Cation interactions: O:R.163, O:R.163 Hydrophobic interactions: I:E.451 NAD.16: 22 residues within 4Å: Chain P: N.72, G.73, F.74, G.75, R.76, I.77, D.100, T.101, D.144, R.145, G.163, T.164, G.165, V.166, F.167, T.187, S.217, C.218, H.245, N.381, E.382, Y.385 12 PLIP interactions: 12 interactions with chain P Hydrogen bonds: P:F.74, P:R.76, P:I.77, P:T.101, P:G.163, P:T.187, P:E.382, P:E.382 Salt bridges: P:R.76, P:R.76 pi-Stacking: P:Y.385 pi-Cation interactions: P: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: ACEGIKMO
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

C
Q

E
A

G
C

I
E

K
G

M
I

O
K

B
P

D
R

F
B

H
D

J
F

L
H

N
J

P
L

Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

Related Entries With Identical Sequence