Research workbench
X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49
Analyse X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UPR
- Type
- protein
- Length
- 1,033 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Toxoplasma gondii (strain ATCC 50611 / Me49)
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- A0A125YP67
- Ligands
- SO4, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · resolution 2 · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 263 | 45% helix, 15% strand | A0A125YP67 |
| B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 258 | 47% helix, 16% strand | A0A125YP67 |
| C | Triosephosphate isomerase (EC 5.3.1.1) | protein | 256 | 47% helix, 16% strand | A0A125YP67 |
| D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 256 | 46% helix, 16% strand | A0A125YP67 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.81 | 0.96 | 43 | empty |
| 2 | 642 | 0.68 | 0.77 | 64 | empty |
| 3 | 138 | 0.44 | 0.76 | 20 | empty |
| 4 | 113 | 0.42 | 0.77 | 19 | empty |
| 5 | 53 | 0.36 | 0.80 | 24 | SO4, CL |
Interfaces
3 interfaces between chains.
- B–C · 1949 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 515 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 365 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5UPR · X-ray structure of a putative triosephosphate isomerase from toxoplasma gondii ME49 · the same entry in another collection · chain A 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 A0A125YP67
- Elsewhere: RCSB PDB 5UPR · PDBe 5UPR · UniProt A0A125YP67
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