Research workbench
Crystal structure of wild-type core streptavidin in complex with D- BIOTIN/BIOTIN-D-sulfoxide at 1.3 a resolution
Analyse Crystal structure of wild-type core streptavidin in complex with D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WYP
- Type
- protein
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- BTN, BSO, SO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 120 | 5% helix, 56% strand | P22629 |
| B, D | Streptavidin | protein | 122 | 2% helix, 55% strand | P22629 |
| C | Streptavidin | protein | 122 | 7% helix, 54% strand | P22629 |
Ligands and binding sites
- BTN · Biotin · ligand · 2 copies · chains A, D
- BSO · Biotin-D-sulfoxide · ligand · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C
- GOL · Glycerol · additive · 10 copies · chains A, D, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.68 | 0.84 | 46 | BSO, GOL |
| 2 | 268 | 0.68 | 0.83 | 48 | BTN, GOL |
| 3 | 444 | 0.64 | 0.78 | 54 | GOL |
| 4 | 172 | 0.54 | 0.80 | 29 | GOL |
| 5 | 159 | 0.54 | 0.80 | 26 | GOL |
Interfaces
6 interfaces between chains.
- D–C · 1629 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1588 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 548 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 545 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 214 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3WYP · Crystal structure of wild-type core streptavidin in complex with… · 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 3WYP · PDBe 3WYP · UniProt P22629
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