MolNFT v1 · #137094 · protein
1.55 ångström resolution crystal structure of glutathione reductase from yersinia pestis in complex with FAD
5VDN · Glutathione oxidoreductase: “1.55 ångström resolution crystal structure of glutathione reductase from yersinia pestis in complex with FAD”. X-ray diffraction, 3 ligands (FAD, BDF, K), 5 pockets (best druggability 0.86). MolNFT v1…
- 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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