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

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

Coordinates

PDB Format

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: 21 residues within 4Å: Chain A: N.10, F.12, G.13, R.14, I.15, N.37, D.38, T.39, R.83, G.101, T.102, G.103, T.125, C.156, N.319, E.320, Y.323 Chain H: E.71, Y.78, D.79, N.80 12 PLIP interactions: 2 interactions with chain H, 10 interactions with chain A Hydrogen bonds: H:Y.78, H:D.79, A:R.14, A:I.15, A:D.38, A:T.39, A:T.39, A:R.83, A:G.103, A:N.319 Hydrophobic interactions: A:I.15, A:Y.323 NAD.2: 19 residues within 4Å: Chain B: F.12, G.13, R.14, I.15, D.38, T.39, R.83, G.101, T.102, G.103, V.104, F.105, T.125, A.126, C.156, N.319, E.320, Y.323 Chain C: S.195 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:S.195, C:S.195, B:F.12, B:R.14, B:I.15, B:T.39, B:R.83, B:N.319 Hydrophobic interactions: B:I.15, B:Y.323 NAD.3: 22 residues within 4Å: Chain C: N.10, F.12, G.13, R.14, I.15, N.37, D.38, T.39, G.101, T.102, G.103, V.104, T.125, A.126, C.156, T.186, N.319, E.320, Y.323 Chain G: E.71, Y.78, N.80 8 PLIP interactions: 2 interactions with chain G, 6 interactions with chain C Hydrogen bonds: G:Y.78, G:N.80, C:F.12, C:F.12, C:R.14, C:I.15 Hydrophobic interactions: C:I.15, C:Y.323 NAD.4: 21 residues within 4Å: Chain A: S.195 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, V.104, F.105, T.125, A.126, S.155, C.156, N.319, Y.323 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.14, D:T.39, D:R.83, D:T.125, A:S.195, A:S.195

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
A

B
B

C
C

D
D

E
I

F
K

G
O

H
P

Glyceraldehyde-3-phosphate dehydrogenase GAPA1

Phosphoribulokinase

Calvin cycle protein CP12-2

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