Research workbench
Crystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase from chlamydomonas reinhardtii (crgapa) complexed with NADP+ and the oxidated catalytic cysteine
Analyse Crystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZQ4
- Type
- protein
- Length
- 684 residues
- Chains
- 2
- 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
- P50362
- Ligands
- NDP, SO4
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| O | Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13) | protein | 338 | 30% helix, 27% strand | P50362 |
| R | Glyceraldehyde-3-phosphate dehydrogenase a, chloroplastic (EC 1.2.1.13) | protein | 346 | 30% helix, 26% strand | P50362 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains O, R
- SO4 · Sulfate ion · ion · 7 copies · chains O, R
- EDO · 1,2-ethanediol · additive · chains O
- GOL · Glycerol · additive · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.76 | 0.79 | 122 | NDP, SO4 |
Interfaces
1 interface between chains.
- O–R · 1396 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7ZQ4 · Crystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase from… · the same entry in another collection · chain O against O, TM-score 1.00
- P50362 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase a… · 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 P50362
- Elsewhere: RCSB PDB 7ZQ4 · PDBe 7ZQ4 · UniProt P50362
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