SMTL ID : 7q57.1

Single Particle Cryo-EM structure of photosynthetic A10B10 glyceraldehyde-3-phospahte dehydrogenase from Spinacia oleracea.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-10-mer

Ligands

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

NAD.1: 21 residues within 4Å: Chain A: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.95, A:Y.406 Hydrogen bonds: A:F.92, A:F.92, A:G.93, A:I.95, A:N.117, A:R.163, A:E.403, A:E.403 NAD.2: 22 residues within 4Å: Chain B: 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, G.100, F.102, T.122, A.123, C.153, T.183, N.316, E.317, Y.320 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.12, B:I.12, B:Y.320 Hydrogen bonds: B:N.7, B:F.9, B:R.11, B:I.12, B:T.36, B:R.80, B:N.316 NAD.3: 20 residues within 4Å: Chain C: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, N.402, E.403, Y.406 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.406 Hydrogen bonds: C:F.92, C:F.92, C:G.93, C:I.95, C:D.118, C:R.163, C:N.402, C:E.403 NAD.4: 22 residues within 4Å: Chain D: 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, G.100, F.102, T.122, C.153, T.183, N.316, E.317, Y.320 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.12, D:I.12, D:Y.320 Hydrogen bonds: D:F.9, D:R.11, D:I.12, D:G.13, D:N.34, D:T.36, D:R.80, D:T.122, D:N.316 NAD.5: 21 residues within 4Å: Chain E: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:I.95, E:Y.406 Hydrogen bonds: E:F.92, E:F.92, E:G.93, E:I.95, E:N.117, E:R.163, E:E.403, E:E.403 NAD.6: 23 residues within 4Å: Chain F: 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, G.100, F.102, T.122, A.123, C.153, T.183, N.316, E.317, Y.320 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:I.12, F:I.12, F:Y.320 Hydrogen bonds: F:N.7, F:F.9, F:R.11, F:I.12, F:G.13, F:T.36, F:R.80, F:N.316 NAD.7: 21 residues within 4Å: Chain G: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:I.95, G:Y.406 Hydrogen bonds: G:F.92, G:G.93, G:I.95, G:D.118, G:R.163, G:T.205, G:N.402, G:E.403 NAD.8: 22 residues within 4Å: 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, G.100, F.102, T.122, C.153, T.183, N.316, E.317, Y.320 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:I.12, H:I.12, H:Y.320 Hydrogen bonds: H:F.9, H:R.11, H:I.12, H:G.13, H:N.34, H:T.36, H:R.80, H:T.122, H:N.316 NAD.9: 21 residues within 4Å: Chain I: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:I.95, I:Y.406 Hydrogen bonds: I:F.92, I:F.92, I:G.93, I:I.95, I:N.117, I:D.118, I:R.163, I:T.205, I:E.403 NAD.10: 23 residues within 4Å: Chain J: 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, G.100, F.102, T.122, A.123, C.153, T.183, N.316, E.317, Y.320 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:I.12, J:I.12, J:Y.320 Hydrogen bonds: J:N.7, J:F.9, J:R.11, J:I.12, J:G.13, J:T.36, J:R.80, J:T.122, J:N.316 NAD.11: 21 residues within 4Å: Chain K: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:I.95, K:Y.406 Hydrogen bonds: K:F.92, K:G.93, K:I.95, K:R.163, K:N.402, K:E.403, K:E.403 NAD.12: 22 residues within 4Å: Chain L: 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, G.100, F.102, T.122, C.153, T.183, N.316, E.317, Y.320 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:I.12, L:I.12, L:Y.320 Hydrogen bonds: L:F.9, L:R.11, L:I.12, L:G.13, L:N.34, L:T.36, L:R.80, L:N.316 NAD.13: 21 residues within 4Å: Chain M: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:I.95, M:Y.406 Hydrogen bonds: M:F.92, M:F.92, M:G.93, M:I.95, M:N.117, M:R.163, M:E.403, M:E.403 NAD.14: 22 residues within 4Å: Chain N: 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, G.100, F.102, T.122, A.123, C.153, T.183, N.316, E.317, Y.320 11 PLIP interactions: 11 interactions with chain N Hydrophobic interactions: N:I.12, N:I.12, N:Y.320 Hydrogen bonds: N:N.7, N:F.9, N:R.11, N:I.12, N:G.13, N:T.36, N:R.80, N:N.316 NAD.15: 21 residues within 4Å: Chain O: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 10 PLIP interactions: 10 interactions with chain O Hydrophobic interactions: O:I.95, O:Y.406 Hydrogen bonds: O:F.92, O:G.93, O:I.95, O:D.118, O:R.163, O:T.205, O:N.402, O:E.403 NAD.16: 22 residues within 4Å: Chain P: 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, G.100, F.102, T.122, C.153, T.183, N.316, E.317, Y.320 12 PLIP interactions: 12 interactions with chain P Hydrophobic interactions: P:I.12, P:I.12, P:Y.320 Hydrogen bonds: P:F.9, P:R.11, P:I.12, P:G.13, P:N.34, P:T.36, P:R.80, P:T.122, P:N.316 NAD.17: 21 residues within 4Å: Chain Q: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 11 PLIP interactions: 11 interactions with chain Q Hydrophobic interactions: Q:I.95, Q:Y.406 Hydrogen bonds: Q:F.92, Q:F.92, Q:G.93, Q:I.95, Q:N.117, Q:D.118, Q:R.163, Q:T.205, Q:E.403 NAD.18: 23 residues within 4Å: Chain R: 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, G.100, F.102, T.122, A.123, C.153, T.183, N.316, E.317, Y.320 12 PLIP interactions: 12 interactions with chain R Hydrophobic interactions: R:I.12, R:I.12, R:Y.320 Hydrogen bonds: R:N.7, R:F.9, R:R.11, R:I.12, R:G.13, R:T.36, R:R.80, R:T.122, R:N.316 NAD.19: 21 residues within 4Å: Chain S: N.90, G.91, F.92, G.93, R.94, I.95, N.117, D.118, R.163, G.181, T.182, G.183, V.184, F.185, T.205, A.206, C.238, T.268, N.402, E.403, Y.406 10 PLIP interactions: 10 interactions with chain S Hydrophobic interactions: S:I.95, S:Y.406 Hydrogen bonds: S:F.92, S:F.92, S:G.93, S:I.95, S:R.163, S:N.402, S:E.403, S:E.403 NAD.20: 22 residues within 4Å: Chain T: 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, G.100, F.102, T.122, C.153, T.183, N.316, E.317, Y.320 11 PLIP interactions: 11 interactions with chain T Hydrophobic interactions: T:I.12, T:I.12, T:Y.320 Hydrogen bonds: T:F.9, T:R.11, T:I.12, T:G.13, T:N.34, T:T.36, T:R.80, T:N.316

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: ACEGIKMOQS
Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic: BDFHJLNPRT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

C
Q

E
A

G
C

I
G

K
E

M
I

O
K

Q
M

S
S

B
P

D
R

F
B

H
D

J
H

L
F

N
J

P
L

R
N

T
T

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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