Research workbench
Traptavidin, apo-form
Analyse Traptavidin, apo-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y3E
- Type
- protein
- Length
- 240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Streptavidin | protein | 120 | 3% helix, 57% strand | P22629 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.47 | 0.81 | 18 | GOL |
| 2 | 95 | 0.46 | 0.80 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 1597 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2Y3E · Traptavidin, apo-form · 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 2Y3E · PDBe 2Y3E · UniProt P22629
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