MolNFT v1 · #114351 · protein
Crystal structure of T75N mutant of triosephosphate isomerase from plasmodium falciparum
5BMX: “Crystal structure of T75N mutant of triosephosphate isomerase from plasmodium falciparum”. X-ray diffraction, 2 ligands (NA, SO4), 11 pockets (best druggability 0.78). MolNFT v1 #114351 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5BMX
- Type
- protein
- Length
- 978 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
- NA, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 247 | 44% helix, 17% strand | Q07412 |
| B, C | Triosephosphate isomerase (EC 5.3.1.1) | protein | 246 | 44% helix, 16% strand | Q07412 |
| D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 239 | 44% helix, 17% strand | Q07412 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.78 | 0.96 | 26 | EDO |
| 2 | 120 | 0.78 | 0.97 | 25 | EDO |
| 3 | 476 | 0.64 | 0.77 | 59 | empty |
| 4 | 89 | 0.58 | 0.87 | 23 | empty |
| 5 | 88 | 0.58 | 0.87 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1751 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1746 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 337 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5BMX · Crystal structure of T75N mutant of Triosephosphate isomerase from Plasmodium falciparum · the same entry in another collection · chain B against B, 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 5BMX · PDBe 5BMX · UniProt Q07412
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