Research workbench
Crystal structure of the thioredoxin reductase from entamoeba histolytica with auranofin AU(I) bound to CYS286
Analyse Crystal structure of the thioredoxin reductase from entamoeba histolytica with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CBQ
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- EC
- 1.8.1.9
- UniProt
- C4LW95
- Ligands
- NDP, FAD, AU, SO4, CL
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thioredoxin reductase (EC 1.8.1.9) | protein | 312 | 27% helix, 29% strand | C4LW95 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- AU · Gold ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.79 | 0.80 | 92 | NDP, FAD |
| 2 | 835 | 0.75 | 0.79 | 88 | NDP, FAD |
| 3 | 329 | 0.60 | 0.78 | 39 | AU, CL |
| 4 | 83 | 0.38 | 0.77 | 16 | NDP |
Interfaces
1 interface between chains.
- A–B · 1577 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4CBQ · Crystal structure of the thioredoxin reductase from Entamoeba histolytica with auranofin… · 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 C4LW95
- Elsewhere: RCSB PDB 4CBQ · PDBe 4CBQ · UniProt C4LW95
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