Research workbench
Crystal structure of glutathionylated glycolytic glyceraldehyde-3- phosphate dehydrogenase from arabidopsis thaliana (ATGAPC1)
Analyse Crystal structure of glutathionylated glycolytic 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
- 6QUQ
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
- EC
- 1.2.1.12
- UniProt
- P25858
- Ligands
- NAD, GSH, SO4
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic (EC 1.2.1.12) | protein | 333 | 31% helix, 28% strand | P25858 |
| R | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic (EC 1.2.1.12) | protein | 334 | 31% helix, 26% strand | P25858 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains O, R
- GSH · Glutathione · ligand · 2 copies · chains O, R
- SO4 · Sulfate ion · ion · 7 copies · chains O, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.77 | 0.79 | 124 | NAD, SO4, GSH |
| 2 | 79 | 0.30 | 0.72 | 16 | SO4 |
Interfaces
1 interface between chains.
- O–R · 1492 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6QUQ · Crystal structure of glutathionylated glycolytic glyceraldehyde-3- phosphate… · the same entry in another collection · chain O against O, TM-score 1.00
- P25858 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase GAPC1… · a predicted model of the same protein · chain O against A, TM-score 0.99
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 P25858
- Elsewhere: RCSB PDB 6QUQ · PDBe 6QUQ · UniProt P25858
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