Research workbench
Crystal structure of thioredoxin reductase from brugia malayi in complex with auranofin
Analyse Crystal structure of thioredoxin reductase from brugia malayi in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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