SMTL ID : 6kez.2 (1 other biounit)

Crystal structure of GAPDH/CP12/PRK complex from Arabidopsis thaliana

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-4-2-2-mer

Ligands

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

NAD.1: 19 residues within 4Å: Chain A: N.10, G.11, G.13, R.14, I.15, D.38, T.39, R.83, G.101, T.102, G.103, T.125, A.126, C.156, H.183, T.186, N.319, Y.323 Chain D: S.195 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:I.15, A:Y.323 Hydrogen bonds: A:R.14, A:I.15, A:D.38, A:R.83, A:R.83, A:T.102, D:S.195, D:S.195, D:S.195 NAD.2: 24 residues within 4Å: Chain B: N.10, F.12, G.13, R.14, I.15, N.37, D.38, T.39, N.82, R.83, G.101, T.102, G.103, T.125, A.126, C.156, T.186, N.319, Y.323 Chain C: S.195 Chain H: E.71, Y.78, D.79, N.80 13 PLIP interactions: 1 interactions with chain H, 11 interactions with chain B, 1 interactions with chain C Hydrogen bonds: H:D.79, B:F.12, B:G.13, B:R.14, B:I.15, B:D.38, B:R.83, B:T.125, B:N.319, C:S.195 Hydrophobic interactions: B:Y.323 Water bridges: B:F.12, B:R.17 NAD.3: 20 residues within 4Å: Chain C: N.10, F.12, G.13, R.14, I.15, N.37, D.38, R.83, G.101, T.102, G.103, F.105, T.125, A.126, C.156, H.183, T.186, N.319, Y.323 Chain H: E.74 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain H Hydrophobic interactions: C:I.15 Hydrogen bonds: C:R.14, C:I.15, C:D.38, C:R.83, C:H.183, H:E.74, H:E.74 pi-Stacking: C:Y.323 NAD.4: 21 residues within 4Å: Chain D: N.10, G.11, G.13, R.14, I.15, N.37, D.38, T.39, R.83, G.101, T.102, G.103, F.105, T.125, A.126, C.156, N.319, E.320 Chain G: E.71, Y.78, N.80 14 PLIP interactions: 1 interactions with chain G, 13 interactions with chain D Hydrogen bonds: G:Y.78, D:G.11, D:R.14, D:I.15, D:N.37, D:T.39, D:T.39, D:R.83, D:R.83, D:T.102, D:T.125, D:N.319 Hydrophobic interactions: D:I.15 pi-Stacking: D:Y.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, A. et al., Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle. Plant Cell (2020)

Release Date

2020-05-13

Peptides

Glyceraldehyde-3-phosphate dehydrogenase GAPA1: ABCD
Phosphoribulokinase: EF
Calvin cycle protein CP12-2: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
J

F
L

G
M

H
N

Glyceraldehyde-3-phosphate dehydrogenase GAPA1

Phosphoribulokinase

Calvin cycle protein CP12-2

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