MolNFT v1 · #185434 · protein
Crystal structure of thioredoxin reductase from brugia malayi in complex with auranofin
7PVJ · Glutaredoxin domain-containing protein: “Crystal structure of thioredoxin reductase from brugia malayi in complex with auranofin”. X-ray diffraction, 4 ligands (FAD, ATR, NA), 19 pockets (best druggability 0.82). MolNFT v1 #185434…
- PDB
- 7PVJ
- Type
- protein
- Length
- 1,695 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaredoxin domain-containing protein
- UniProt
- A0A0J9XPH7
- Ligands
- FAD, ATR, NA, AU
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaredoxin domain-containing protein | protein | 577 | 37% helix, 25% strand | A0A0J9XPH7 |
| B | Glutaredoxin domain-containing protein | protein | 577 | 37% helix, 25% strand | A0A0J9XPH7 |
| C | Glutaredoxin domain-containing protein | protein | 541 | 39% helix, 21% strand | A0A0J9XPH7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
- ATR · 2'-monophosphoadenosine-5'-diphosphate · ligand · chains A
- NA · Sodium ion · metal · chains A
- AU · Gold ion · metal · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.82 | 0.84 | 109 | FAD, ATR, NA |
| 2 | 862 | 0.81 | 0.84 | 110 | FAD, MPD |
| 3 | 194 | 0.80 | 0.95 | 53 | empty |
| 4 | 1186 | 0.80 | 0.81 | 121 | FAD |
| 5 | 130 | 0.78 | 0.96 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3701 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 364 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7PVJ · Crystal structure of Thioredoxin Reductase from Brugia Malayi in complex 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 A0A0J9XPH7
- Elsewhere: RCSB PDB 7PVJ · PDBe 7PVJ · UniProt A0A0J9XPH7
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