Research workbench
2.3 ångström resolution crystal structure of glutathione reductase from vibrio parahaemolyticus in complex with FAD.
Analyse 2.3 ångström resolution crystal structure of glutathione reductase from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U1O
- Type
- protein
- Length
- 1,802 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione reductase
- UniProt
- Q87TK1
- Ligands
- FAD, SO4, CL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glutathione reductase | protein | 450 | 35% helix, 28% strand | Q87TK1 |
| B, C | Glutathione reductase | protein | 451 | 35% helix, 27% strand | Q87TK1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.86 | 0.87 | 142 | empty |
| 2 | 1013 | 0.85 | 0.86 | 150 | empty |
| 3 | 812 | 0.79 | 0.82 | 92 | FAD |
| 4 | 791 | 0.79 | 0.82 | 91 | FAD, CL |
| 5 | 829 | 0.78 | 0.81 | 97 | FAD |
Interfaces
6 interfaces between chains.
- A–B · 3612 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 3580 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 423 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 410 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5U1O · 2.3 Angstrom Resolution Crystal Structure of Glutathione Reductase from Vibrio… · 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 Q87TK1
- Elsewhere: RCSB PDB 5U1O · PDBe 5U1O · UniProt Q87TK1
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