Research workbench
Wild-type core streptavidin at atomic resolution
Analyse Wild-type core streptavidin at atomic resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RY1
- Type
- protein
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 122 | 5% helix, 54% strand | P22629 |
| B | Streptavidin | protein | 126 | 7% helix, 54% strand | P22629 |
| C | Streptavidin | protein | 121 | 5% helix, 55% strand | P22629 |
| D | Streptavidin | protein | 121 | 5% helix, 55% strand | P22629 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 7 copies · chains A, D, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, D, B
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 | 532 | 0.69 | 0.79 | 55 | MRD |
| 2 | 405 | 0.63 | 0.77 | 49 | MRD, MPD |
| 3 | 141 | 0.59 | 0.83 | 29 | MPD, MRD |
| 4 | 187 | 0.54 | 0.79 | 30 | empty |
| 5 | 193 | 0.49 | 0.76 | 21 | MRD, MPD |
Interfaces
6 interfaces between chains.
- A–B · 1621 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1541 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 480 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 394 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 201 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3RY1 · Wild-type core streptavidin at atomic resolution · 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 3RY1 · PDBe 3RY1 · UniProt P22629
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