Research workbench
1.55 ångström resolution crystal structure of glutathione reductase from yersinia pestis in complex with FAD
Analyse 1.55 ångström resolution crystal structure of glutathione reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VDN
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione oxidoreductase
- EC
- 1.8.1.7
- UniProt
- Q8CZL0
- Ligands
- FAD, BDF, K
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutathione oxidoreductase (EC 1.8.1.7) | protein | 449 | 37% helix, 27% strand | Q8CZL0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- BDF · beta-D-fructopyranose · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.86 | 0.92 | 53 | empty |
| 2 | 827 | 0.79 | 0.82 | 101 | FAD, BDF |
| 3 | 749 | 0.77 | 0.81 | 88 | FAD, BDF |
| 4 | 237 | 0.72 | 0.87 | 41 | K |
| 5 | 223 | 0.71 | 0.87 | 37 | K |
Interfaces
1 interface between chains.
- A–B · 3567 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5VDN · 1.55 Angstrom Resolution Crystal Structure of Glutathione Reductase from Yersinia pestis… · 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 Q8CZL0
- Elsewhere: RCSB PDB 5VDN · PDBe 5VDN · UniProt Q8CZL0
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