Research workbench
Crystal structure of thioredoxin reductase from brugia malayi in complex with NADP(H)
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
- 7PUT
- Type
- protein
- Length
- 1,693 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaredoxin domain-containing protein | protein | 578 | 35% helix, 25% strand | A0A0J9XPH7 |
| B | Glutaredoxin domain-containing protein | protein | 575 | 36% helix, 24% strand | A0A0J9XPH7 |
| C | Glutaredoxin domain-containing protein | protein | 540 | 36% helix, 20% 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
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.81 | 0.83 | 110 | FAD, ATR |
| 2 | 832 | 0.81 | 0.83 | 112 | FAD, MPD |
| 3 | 1197 | 0.79 | 0.80 | 127 | FAD |
| 4 | 144 | 0.79 | 0.96 | 47 | empty |
| 5 | 116 | 0.78 | 0.97 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3713 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 241 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 7PUT · Crystal structure of Thioredoxin Reductase from Brugia Malayi in complex with NADP(H) · 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 7PUT · PDBe 7PUT · UniProt A0A0J9XPH7
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