Research workbench
Crystal structure of human glutathione reductase complexed with a fluoro-analogue of the menadione derivative M5
Analyse Crystal structure of human glutathione reductase complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GH5
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione reductase, mitochondrial
- EC
- 1.8.1.7
- UniProt
- P00390
- Ligands
- ELI, FAD, PO4
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione reductase, mitochondrial (EC 1.8.1.7) | protein | 461 | 34% helix, 25% strand | P00390 |
Ligands and binding sites
- ELI · 6-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)hexanoic acid · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.87 | 0.88 | 101 | GOL, ELI |
| 2 | 1044 | 0.79 | 0.81 | 117 | PO4, FAD, GOL |
| 3 | 964 | 0.79 | 0.81 | 110 | PO4, FAD, GOL |
| 4 | 319 | 0.70 | 0.83 | 38 | ELI, GOL |
Interfaces
1 interface between chains.
- A–B · 3331 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 2GH5 · Crystal Structure of human Glutathione Reductase complexed with a Fluoro-Analogue of the… · the same entry in another collection · chain A against A, TM-score 1.00
- P00390 · AlphaFold monomer V2.0 prediction for glutathione reductase, mitochondrial (P00390) · a predicted model of the same protein · 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 P00390
- Elsewhere: RCSB PDB 2GH5 · PDBe 2GH5 · UniProt P00390
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