MolNFT v1 · #128169 · protein
Crystal structure of the atypical thioredoxin reductase tri from desulfovibrio vulgaris hildenborough
5NII: “Crystal structure of the atypical thioredoxin reductase tri from desulfovibrio vulgaris hildenborough”. X-ray diffraction, 3 ligands (FAD, NA, CL), 6 pockets (best druggability 0.69). MolNFT v1 #128169 on GenesisL1: 3D structure…
- PDB
- 5NII
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- UniProt
- Q72C27
- Ligands
- FAD, NA, CL
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase | protein | 296 | 31% helix, 25% strand | Q72C27 |
| B | Thioredoxin reductase | protein | 298 | 31% helix, 23% strand | Q72C27 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.69 | 0.81 | 45 | FAD |
| 2 | 379 | 0.64 | 0.79 | 41 | FAD |
| 3 | 67 | 0.52 | 0.86 | 22 | empty |
| 4 | 138 | 0.51 | 0.79 | 18 | empty |
| 5 | 158 | 0.48 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1606 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5NII · Crystal structure of the atypical thioredoxin reductase TRi from Desulfovibrio vulgaris… · 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 Q72C27
- Elsewhere: RCSB PDB 5NII · PDBe 5NII · UniProt Q72C27
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