Research workbench
Crystal structure of the human glutaredoxin 5 with bound glutathione in an fes cluster
Analyse Crystal structure of the human glutaredoxin 5 with bound glutathione in an fes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WUL
- Type
- protein
- Length
- 436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaredoxin related protein 5
- UniProt
- Q86SX6
- Ligands
- GSH, FES, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glutaredoxin related protein 5 | protein | 109 | 47% helix, 17% strand | Q86SX6 |
| C | Glutaredoxin related protein 5 | protein | 109 | 49% helix, 17% strand | Q86SX6 |
Ligands and binding sites
- GSH · Glutathione · ligand · 4 copies · chains A, B, D, C
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.76 | 0.78 | 84 | GSH, FES |
| 2 | 132 | 0.38 | 0.73 | 25 | PEG |
| 3 | 93 | 0.34 | 0.73 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–D · 419 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 401 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 305 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 300 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2WUL · Crystal structure of the human glutaredoxin 5 with bound glutathione in an fes cluster · the same entry in another collection · chain A against A, TM-score 1.00
- Q86SX6 · AlphaFold monomer V2.0 prediction for glutaredoxin-related protein 5, mitochondrial… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q86SX6
- Elsewhere: RCSB PDB 2WUL · PDBe 2WUL · UniProt Q86SX6
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