Research workbench
Crystal structure of ALIS3-streptavidin complex
Analyse Crystal structure of ALIS3-streptavidin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B5F
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- 6F3
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Streptavidin | protein | 120 | 5% helix, 57% strand | P22629 |
Ligands and binding sites
- 6F3 · N-methyl-3-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)benzenesulfonamide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.59 | 0.85 | 25 | 6F3 |
| 2 | 163 | 0.54 | 0.80 | 26 | empty |
| 3 | 174 | 0.54 | 0.80 | 26 | empty |
| 4 | 174 | 0.52 | 0.79 | 32 | empty |
| 5 | 171 | 0.52 | 0.79 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1624 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1618 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 416 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 212 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5B5F · Crystal structure of ALiS3-Streptavidin complex · 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 5B5F · PDBe 5B5F · UniProt P22629
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