MolNFT v1 · #126525 · protein
Thioredoxin reductase from giardia duodenalis
5M5J: “Thioredoxin reductase from giardia duodenalis”. X-ray diffraction, 2 ligands (FAD, NA), 5 pockets (best druggability 0.79). MolNFT v1 #126525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M5J
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- EC
- 1.8.1.9
- UniProt
- E2RU27
- Ligands
- FAD, NA
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase (EC 1.8.1.9) | protein | 309 | 24% helix, 30% strand | E2RU27 |
| B | Thioredoxin reductase (EC 1.8.1.9) | protein | 312 | 25% helix, 30% strand | E2RU27 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.79 | 0.89 | 55 | FAD |
| 2 | 1007 | 0.77 | 0.79 | 103 | FAD |
| 3 | 249 | 0.72 | 0.87 | 45 | empty |
| 4 | 354 | 0.61 | 0.78 | 60 | empty |
| 5 | 178 | 0.49 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2105 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M5J · Thioredoxin reductase from Giardia duodenalis · 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 E2RU27
- Elsewhere: RCSB PDB 5M5J · PDBe 5M5J · UniProt E2RU27
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