Research workbench
Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin
Analyse Crystallographic and thermodynamic comparison of natural and synthetic ligands… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SRE
- Type
- protein
- Length
- 235 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- HAB
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 116 | 5% helix, 59% strand | P22629 |
| B | Streptavidin | protein | 119 | 5% helix, 56% strand | P22629 |
Ligands and binding sites
- HAB · 2-((4'-hydroxyphenyl)-azo)benzoic acid · ligand · 2 copies · chains A, B
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 | 104 | 0.48 | 0.80 | 17 | HAB |
| 2 | 87 | 0.46 | 0.80 | 18 | HAB |
| 3 | 50 | 0.30 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1614 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1SRE · Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to… · 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 1SRE · PDBe 1SRE · UniProt P22629
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