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Crystal structure of photosynthetic A4 isoform glyceraldehyde-3- phosphate dehydrogenase complexed with NAD, from arabidopsis thaliana

Analyse Crystal structure of photosynthetic A4 isoform glyceraldehyde-3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3K2B
Type: protein
Length: 3,363 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic
EC: 1.2.1.13
UniProt: P25856
Ligands: NAD, SO4
Pockets: 18 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, O	Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13)	protein	337	32% helix, 26% strand	P25856
D, F, G, Q	Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13)	protein	336	29% helix, 24% strand	P25856
E	Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13)	protein	336	27% helix, 25% strand	P25856
H	Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13)	protein	335	25% helix, 26% strand	P25856

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 10 copies · chains A, D, B, C, E, F, G, H, O, Q
SO4 · Sulfate ion · ion · 45 copies · chains A, B, C, E, D, F, G, H, O, Q

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

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	753	0.80	0.83	95	empty
2	701	0.79	0.83	89	empty
3	1150	0.77	0.79	130	NAD, SO4
4	1013	0.77	0.80	111	NAD, SO4
5	1102	0.77	0.79	127	NAD, SO4

Interfaces

18 interfaces between chains.

O–Q · 1991 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 1983 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 1982 Å² buried · 33 hydrogen bonds · protein-protein
F–H · 1960 Å² buried · 38 hydrogen bonds · protein-protein
E–G · 1782 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

3K2B · Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase… · the same entry in another collection · chain Q against Q, TM-score 1.00
P25856 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase GAPA1… · a predicted model of the same protein · chain O against A, 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
Elsewhere: RCSB PDB 3K2B · PDBe 3K2B · UniProt P25856

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