SMTL ID : 7q56.1

Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-8-mer

Ligands

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

NAD.1: 19 residues within 4Å: Chain B: G.8, F.9, G.10, R.11, I.12, R.14, D.35, R.80, G.98, T.99, V.101, T.122, A.123, C.153, D.185, N.316, E.317, Y.320 Chain C: S.194 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.320 Hydrogen bonds: B:F.9, B:F.9, B:R.11, B:I.12, B:R.14, B:R.14, B:R.80, B:T.99, B:C.153, B:D.185, B:N.316, C:S.194, C:S.194 Salt bridges: B:R.11, B:R.14 NAD.2: 17 residues within 4Å: Chain C: F.9, G.10, R.11, I.12, N.34, N.79, R.80, G.98, T.99, V.101, T.122, D.187, N.319, E.320 Chain O: E.362, Y.367, E.368 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain O Hydrophobic interactions: C:E.320 Hydrogen bonds: C:F.9, C:F.9, C:R.11, C:I.12, C:N.34, C:R.80, C:R.80, C:T.122, C:D.187, C:D.187, C:E.320, C:E.320, O:Y.367 pi-Cation interactions: C:R.80 NAD.3: 19 residues within 4Å: Chain C: Y.367, E.368 Chain O: G.8, F.9, G.10, R.11, I.12, R.14, N.34, N.79, R.80, G.98, T.99, V.101, T.122, D.187, N.319, E.320, Y.323 15 PLIP interactions: 14 interactions with chain O, 1 interactions with chain C Hydrophobic interactions: O:I.12, O:I.12, O:Y.323, O:Y.323 Hydrogen bonds: O:F.9, O:R.11, O:I.12, O:R.14, O:R.14, O:N.34, O:R.80, O:R.80, O:R.80, O:E.320, C:E.368 NAD.4: 24 residues within 4Å: Chain A: R.189, A.193, S.194 Chain D: N.7, G.8, G.10, R.11, I.12, G.13, N.34, D.35, T.36, D.79, R.80, G.98, T.99, T.122, A.123, S.152, C.153, H.180, R.234, N.316, Y.320 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.123, D:Y.320 Hydrogen bonds: D:G.8, D:R.11, D:R.11, D:I.12, D:G.13, D:N.34, D:D.35, D:T.36, D:T.36, D:D.79, D:R.80, D:G.98, D:C.153, D:R.234, D:N.316, A:R.189, A:S.194 NAD.5: 22 residues within 4Å: Chain E: N.7, G.8, F.9, G.10, R.11, I.12, G.13, R.14, N.34, N.79, R.80, G.98, T.99, V.101, T.122, P.124, N.152, N.319, E.320, Y.323 Chain M: Y.367, E.368 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain M Hydrophobic interactions: E:Y.323 Hydrogen bonds: E:R.11, E:G.13, E:R.14, E:R.14, E:N.34, E:R.80, E:E.320, M:E.368 Salt bridges: E:R.14 pi-Cation interactions: E:R.80 NAD.6: 20 residues within 4Å: Chain F: G.8, F.9, G.10, R.11, I.12, G.13, R.14, D.35, R.80, G.98, T.99, V.101, T.122, A.123, C.153, D.185, N.316, E.317, Y.320 Chain G: S.194 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:Y.320 Hydrogen bonds: F:F.9, F:R.11, F:I.12, F:G.13, F:R.80, F:T.99, F:C.153, F:D.185, F:N.316, G:S.194, G:S.194 Salt bridges: F:R.14 NAD.7: 17 residues within 4Å: Chain G: F.9, G.10, R.11, I.12, G.13, N.34, N.79, R.80, G.98, T.99, V.101, T.122, N.319, E.320, Y.323 Chain K: Y.367, E.368 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:I.12, G:Y.323, G:Y.323 Hydrogen bonds: G:G.10, G:R.11, G:I.12, G:G.13, G:N.34, G:R.80, G:E.320 pi-Cation interactions: G:R.80, G:R.80 NAD.8: 25 residues within 4Å: Chain E: R.189, A.193, S.194 Chain H: N.7, G.8, F.9, G.10, R.11, I.12, G.13, N.34, D.35, T.36, D.79, R.80, G.98, T.99, T.122, A.123, S.152, C.153, H.180, R.234, N.316, Y.320 18 PLIP interactions: 16 interactions with chain H, 2 interactions with chain E Hydrophobic interactions: H:A.123, H:Y.320 Hydrogen bonds: H:G.8, H:F.9, H:R.11, H:G.13, H:N.34, H:D.35, H:T.36, H:T.36, H:D.79, H:R.80, H:G.98, H:C.153, H:R.234, H:N.316, E:R.189, E:S.194 NAD.9: 21 residues within 4Å: Chain A: N.7, G.8, F.9, G.10, R.11, I.12, R.14, N.34, N.79, R.80, G.98, T.99, V.101, F.102, T.122, D.187, E.320, Y.323 Chain I: A.360, K.365, E.368 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.7, A:F.9, A:R.11, A:I.12, A:R.14, A:R.14, A:N.34, A:R.80, A:R.80, A:R.80, A:D.187, A:E.320 Salt bridges: A:R.14 pi-Cation interactions: A:R.80, A:R.80 NAD.10: 21 residues within 4Å: Chain A: Y.367, E.368 Chain I: G.8, F.9, G.10, R.11, I.12, G.13, N.15, N.34, S.36, N.79, R.80, G.98, T.99, A.123, P.124, C.155, N.319, E.320, Y.323 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:A.123, I:Y.323 Hydrogen bonds: I:F.9, I:R.11, I:G.13, I:N.15, I:N.34, I:S.36, I:N.79, I:C.155, I:N.319, I:E.320 NAD.11: 23 residues within 4Å: Chain J: N.7, G.8, F.9, G.10, R.11, I.12, N.34, D.35, T.36, D.79, R.80, G.98, T.99, V.101, F.102, T.122, A.123, S.152, C.153, H.180, T.183, D.185, Y.320 17 PLIP interactions: 17 interactions with chain J Hydrophobic interactions: J:T.122, J:A.123, J:Y.320 Hydrogen bonds: J:G.8, J:F.9, J:R.11, J:I.12, J:R.14, J:N.34, J:T.36, J:T.36, J:R.80, J:C.153, J:T.183, J:T.183, J:G.184, J:D.185 NAD.12: 19 residues within 4Å: Chain G: E.368 Chain K: N.7, G.8, F.9, G.10, R.11, I.12, R.14, N.34, N.79, R.80, G.98, T.99, V.101, T.122, D.187, N.319, E.320, Y.323 13 PLIP interactions: 13 interactions with chain K Hydrophobic interactions: K:I.12, K:Y.323 Hydrogen bonds: K:G.10, K:R.11, K:I.12, K:R.14, K:N.34, K:R.80, K:R.80, K:T.185, K:D.187, K:E.320 Salt bridges: K:R.14 NAD.13: 17 residues within 4Å: Chain L: G.8, F.9, G.10, R.11, I.12, G.13, N.34, D.35, T.36, R.80, G.98, T.99, T.122, C.153, D.185, N.316, Y.320 16 PLIP interactions: 16 interactions with chain L Hydrophobic interactions: L:Y.320 Hydrogen bonds: L:G.8, L:G.10, L:R.11, L:I.12, L:G.13, L:N.34, L:N.34, L:T.36, L:R.80, L:T.122, L:D.185, L:D.185, L:N.316 Salt bridges: L:R.11, L:R.11 NAD.14: 23 residues within 4Å: Chain E: A.360, Y.367, E.368 Chain M: G.8, F.9, G.10, R.11, I.12, G.13, N.34, N.79, R.80, G.98, T.99, V.101, A.123, P.124, S.154, C.155, T.156, N.319, E.320, Y.323 15 PLIP interactions: 1 interactions with chain E, 14 interactions with chain M Hydrogen bonds: E:E.368, M:F.9, M:R.11, M:G.13, M:N.34, M:R.80, M:C.155, M:T.156, M:N.319, M:E.320, M:E.320 Hydrophobic interactions: M:A.123, M:Y.323 pi-Cation interactions: M:R.80, M:R.80 NAD.15: 22 residues within 4Å: Chain N: G.8, F.9, G.10, R.11, I.12, R.14, N.34, T.36, D.79, R.80, G.98, T.99, F.102, T.122, A.123, S.152, C.153, T.183, G.184, D.185, Y.320 Chain O: S.194 18 PLIP interactions: 17 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:T.122, N:A.123, N:Y.320 Hydrogen bonds: N:F.9, N:R.11, N:I.12, N:R.14, N:R.80, N:R.80, N:C.153, N:T.183, N:T.183, N:G.184, N:D.185, N:N.316, O:S.194 pi-Cation interactions: N:R.80, N:R.80 NAD.16: 19 residues within 4Å: Chain P: N.7, G.8, G.10, R.11, I.12, G.13, R.14, N.34, D.35, T.36, D.79, R.80, G.98, T.99, T.122, C.153, D.185, N.316, Y.320 12 PLIP interactions: 12 interactions with chain P Hydrophobic interactions: P:Y.320 Hydrogen bonds: P:R.11, P:I.12, P:G.13, P:N.34, P:T.36, P:D.79, P:R.80, P:T.122, P:D.185, P:N.316 Salt bridges: P:R.14

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
I

C
K

E
A

G
C

I
Q

K
O

M
G

O
E

B
J

D
L

F
B

H
D

J
R

L
P

N
H

P
F

Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

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