Research workbench
Rapid crystallization of streptavidin using charged peptides
Analyse Rapid crystallization of streptavidin using charged peptides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LNG
- Type
- protein
- Length
- 732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Streptomyces avidinii
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Streptavidin | protein | 122 | 5% helix, 56% strand | P22629 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, D, B, C, E, F
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 | 731 | 0.72 | 0.78 | 82 | GOL |
| 2 | 552 | 0.66 | 0.77 | 60 | GOL |
| 3 | 352 | 0.63 | 0.79 | 44 | GOL |
| 4 | 343 | 0.56 | 0.75 | 42 | GOL |
| 5 | 187 | 0.52 | 0.77 | 23 | GOL |
Interfaces
9 interfaces between chains.
- C–D · 1674 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1642 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 395 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 394 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 393 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6LNG · Rapid crystallization of streptavidin using charged peptides · 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 P22629
- Elsewhere: RCSB PDB 6LNG · PDBe 6LNG · UniProt P22629
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