MolNFT v1 · #114374 · protein
Crystal structure of T75C mutant of triosephosphate isomerase from plasmodium falciparum
5BNK: “Crystal structure of T75C mutant of triosephosphate isomerase from plasmodium falciparum”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.74). MolNFT v1 #114374 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5BNK
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q07412
- Ligands
- NA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 244 | 45% helix, 16% strand | Q07412 |
| B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 235 | 42% helix, 17% strand | Q07412 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.74 | 0.83 | 57 | empty |
| 2 | 126 | 0.43 | 0.76 | 27 | EDO |
| 3 | 84 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1137 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5BNK · Crystal structure of T75C mutant of Triosephosphate isomerase from Plasmodium falciparum · 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 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 5BNK · PDBe 5BNK · UniProt Q07412
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