Research workbench
Crystal structure of thioredoxin reductase from cryptococcus neoformans in complex with FAD (fo conformation)
Analyse Crystal structure of thioredoxin reductase from cryptococcus neoformans in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W4C
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- EC
- 1.8.1.9
- UniProt
- J9VRX9
- Ligands
- FAD, CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase (EC 1.8.1.9) | protein | 356 | 28% helix, 25% strand | J9VRX9 |
| B | Thioredoxin reductase (EC 1.8.1.9) | protein | 338 | 29% helix, 26% strand | J9VRX9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.79 | 0.81 | 93 | FAD, PEG |
| 2 | 589 | 0.78 | 0.84 | 78 | FAD |
| 3 | 449 | 0.73 | 0.83 | 47 | GOL |
| 4 | 112 | 0.47 | 0.80 | 25 | empty |
| 5 | 62 | 0.32 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2720 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5W4C · Crystal structure of thioredoxin reductase from Cryptococcus neoformans in complex with… · 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 J9VRX9
- Elsewhere: RCSB PDB 5W4C · PDBe 5W4C · UniProt J9VRX9
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