Research workbench
Structure of a novel oxidoreductase from Gloeobacter violaceus
Analyse Structure of a novel oxidoreductase from Gloeobacter violaceus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ODE
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.196
- Source
- Gloeobacter violaceus
- Molecule
- Gll2934 protein
- UniProt
- Q7NCP4
- Ligands
- FAD, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.196 · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gll2934 protein | protein | 324 | 28% helix, 28% strand | Q7NCP4 |
| B | Gll2934 protein | protein | 322 | 29% helix, 27% strand | Q7NCP4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 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 | 431 | 0.81 | 0.89 | 61 | FAD, SO4 |
| 2 | 405 | 0.81 | 0.89 | 57 | FAD |
| 3 | 648 | 0.69 | 0.77 | 61 | SO4 |
| 4 | 360 | 0.57 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2929 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ODE · Structure of a novel oxidoreductase from gloeobacter violaceus · 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 Q7NCP4
- Elsewhere: RCSB PDB 5ODE · PDBe 5ODE · UniProt Q7NCP4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.