Research workbench
Crystal structure of ALIS2-streptavidin complex
Analyse Crystal structure of ALIS2-streptavidin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y5D
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- MT6
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Streptavidin | protein | 122 | 5% helix, 54% strand | P22629 |
Ligands and binding sites
- MT6 · methyl 3-(4-oxo-4,5-dihydrofuro[3,2-c]pyridin-2-yl)benzoate · ligand · 3 copies · chains A, D, B, C
- P6G · Hexaethylene glycol · additive · 2 copies · chains B, C
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.68 | 0.79 | 60 | DMS, P6G |
| 2 | 439 | 0.63 | 0.77 | 47 | MT6 |
| 3 | 132 | 0.58 | 0.83 | 26 | MT6 |
| 4 | 200 | 0.54 | 0.79 | 28 | empty |
| 5 | 113 | 0.45 | 0.78 | 18 | MT6 |
Interfaces
6 interfaces between chains.
- A–B · 1617 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1572 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 489 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 384 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 216 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4Y5D · CRYSTAL STRUCTURE OF ALiS2-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 4Y5D · PDBe 4Y5D · UniProt P22629
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