Research workbench
Y74COX mutant of plasmodium falciparum triosephosphate isomerase
Analyse Y74COX mutant of plasmodium falciparum triosephosphate isomerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GZP
- Type
- protein
- Length
- 492 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.03
- Source
- Plasmodium falciparum
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q07412
- Ligands
- PGA
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.03 · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 246 | 44% helix, 16% strand | Q07412 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.81 | 0.96 | 28 | EDO |
| 2 | 146 | 0.47 | 0.77 | 22 | empty |
| 3 | 57 | 0.37 | 0.79 | 11 | empty |
| 4 | 63 | 0.33 | 0.76 | 18 | empty |
| 5 | 79 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1307 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5GZP · Y74COX mutant of plasmodium falciparum triosephosphate isomerase · the same entry in another collection · chain A against A, TM-score 1.00
- Q07412 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (Q07412) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q07412
- Elsewhere: RCSB PDB 5GZP · PDBe 5GZP · UniProt Q07412
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