MolNFT v1 · #22155 · protein
Streptavidin mutant Y43F
1SWU: “Streptavidin mutant Y43F”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1 #22155 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SWU
- Type
- protein
- Length
- 465 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 120 | 5% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 116 | 8% helix, 57% strand | P22629 |
| C | Streptavidin | protein | 114 | 5% helix, 59% strand | P22629 |
| D | Streptavidin | protein | 115 | 8% helix, 57% strand | P22629 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, D, B, C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, D
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 | 592 | 0.70 | 0.78 | 64 | MPD |
| 2 | 348 | 0.62 | 0.78 | 40 | MPD |
| 3 | 152 | 0.60 | 0.83 | 29 | MRD, MPD |
| 4 | 162 | 0.52 | 0.80 | 30 | empty |
| 5 | 133 | 0.46 | 0.77 | 16 | MPD |
Interfaces
6 interfaces between chains.
- A–B · 1641 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1600 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 410 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 204 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1SWU · Streptavidin mutant Y43F · 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 1SWU · PDBe 1SWU · UniProt P22629
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