Research workbench
Structure-based design of synthetic azobenzene ligands for streptavidin
Analyse Structure-based design of synthetic azobenzene ligands for streptavidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SRG
- Type
- protein
- Length
- 232 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Streptomyces avidinii
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- MHB
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 5% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Streptavidin | protein | 116 | 5% helix, 59% strand | P22629 |
Ligands and binding sites
- MHB · 2-((3'-methyl-4'-hydroxyphenyl)azo)benzoic acid · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.48 | 0.80 | 19 | MHB |
| 2 | 98 | 0.48 | 0.80 | 19 | MHB |
| 3 | 58 | 0.32 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1600 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
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 P22629
- Elsewhere: RCSB PDB 1SRG · PDBe 1SRG · UniProt P22629
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