Research workbench
Crystal structure of the non-regulatory A4 isoform of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase complexed with NADP
Analyse Crystal structure of the non-regulatory A4 isoform of spinach chloroplast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JN0
- Type
- protein
- Length
- 1,002 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase a
- EC
- 1.2.1.13
- UniProt
- P19866
- Ligands
- NDP, SO4
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O, A, B | Glyceraldehyde-3-phosphate dehydrogenase a (EC 1.2.1.13) | protein | 334 | 31% helix, 27% strand | P19866 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains O, A, B
- SO4 · Sulfate ion · ion · 6 copies · chains O, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.77 | 0.79 | 124 | SO4, NDP |
| 2 | 451 | 0.63 | 0.77 | 48 | SO4, NDP |
Interfaces
1 interface between chains.
- A–B · 1265 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1JN0 · Crystal structure of the non-regulatory A4 isoform of spinach chloroplast… · the same entry in another collection · chain O against O, TM-score 1.00
- P19866 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase a… · a predicted model of the same protein · chain B 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 P19866
- Elsewhere: RCSB PDB 1JN0 · PDBe 1JN0 · UniProt P19866
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