Research workbench
Crystal structure of the F96H mutant of plasmodium falciparum triosephosphate isomerase with 3- phosphoglycerate bound at the dimer interface
Analyse Crystal structure of the F96H mutant of plasmodium falciparum triosephosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VFG
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q07412
- Ligands
- 3PG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Triosephosphate isomerase (EC 5.3.1.1) | protein | 247 | 43% helix, 17% strand | Q07412 |
| B, D | 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, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.80 | 0.94 | 40 | 3PG |
| 2 | 227 | 0.78 | 0.92 | 40 | 3PG |
| 3 | 200 | 0.43 | 0.73 | 37 | empty |
| 4 | 100 | 0.43 | 0.78 | 23 | empty |
| 5 | 75 | 0.39 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1792 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1783 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 371 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2VFG · Crystal structure of the F96H 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 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 Q07412
- Elsewhere: RCSB PDB 2VFG · PDBe 2VFG · UniProt Q07412
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