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

Analyse Crystal structure of GAPDH/CP12/PRK complex from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KEZ
Type: protein
Length: 4,345 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase GAPA1; Phosphoribulokinase; Calvin cycle protein…
EC: 1.2.1.13, 2.7.1.19
UniProt: P25856, P25697, Q9LZP9
Ligands: NAD
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F, G, H	Glyceraldehyde-3-phosphate dehydrogenase GAPA1 (EC 1.2.1.13)	protein	336	31% helix, 28% strand	P25856
D	Glyceraldehyde-3-phosphate dehydrogenase GAPA1 (EC 1.2.1.13)	protein	335	28% helix, 28% strand	P25856
I, K, J, L	Phosphoribulokinase (EC 2.7.1.19)	protein	342	35% helix, 25% strand	P25697
M, N	Calvin cycle protein CP12-2	protein	73	70% helix, 0% strand	Q9LZP9
O, P	Calvin cycle protein CP12-2	protein	72	72% helix, 0% strand	Q9LZP9

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, D, P, B, C, O, E, H, M, F, G, N

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1033	0.83	0.84	107	NAD
2	1091	0.83	0.84	118	NAD
3	1023	0.82	0.84	102	empty
4	709	0.81	0.85	78	empty
5	912	0.81	0.83	103	empty

Interfaces

34 interfaces between chains.

A–C · 1991 Å² buried · 16 hydrogen bonds · protein-protein
E–G · 1979 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 1963 Å² buried · 29 hydrogen bonds · protein-protein
F–H · 1960 Å² buried · 30 hydrogen bonds · protein-protein
F–G · 1400 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide (disulfide).

Compared structures

6KEZ · Crystal structure of GAPDH/CP12/PRK complex from Arabidopsis thaliana · the same entry in another collection · chain J against J, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P25856
Every structure of UniProt P25697
Every structure of UniProt Q9LZP9
Elsewhere: RCSB PDB 6KEZ · PDBe 6KEZ · UniProt P25856 · UniProt P25697 · UniProt Q9LZP9

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