Research workbench
Crystal structure of the Plasmodium falciparum triosephosphate isomerase in the loop closed state with 3-phosphoglycerate bound at the active site and interface
Analyse Crystal structure of the Plasmodium falciparum triosephosphate isomerase in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VFI
- Type
- protein
- Length
- 492 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- PLASMODIUM FALCIPARUM
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q07412
- Ligands
- 3PG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.25 · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 246 | 43% helix, 17% strand | Q07412 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.75 | 0.96 | 26 | empty |
| 2 | 93 | 0.61 | 0.88 | 22 | 3PG |
| 3 | 58 | 0.51 | 0.87 | 20 | 3PG |
| 4 | 82 | 0.50 | 0.84 | 27 | 3PG |
| 5 | 51 | 0.26 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1774 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2VFI · Crystal structure of the plasmodium falciparum triosephosphate isomerase in the loop… · 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 0.99
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 Q07412
- Elsewhere: RCSB PDB 2VFI · PDBe 2VFI · UniProt Q07412
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