MolNFT v1 · #15606 · protein
Streptavidin mutant S27A at 1.5A resolution
1N9Y: “Streptavidin mutant S27A at 1.5A resolution”. X-ray diffraction, 3 pockets (best druggability 0.72). MolNFT v1 #15606 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1N9Y
- Type
- protein
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 118 | 8% helix, 57% strand | P22629 |
| B | Streptavidin | protein | 118 | 8% helix, 56% strand | P22629 |
| C | Streptavidin | protein | 117 | 5% helix, 57% strand | P22629 |
| D | Streptavidin | protein | 119 | 8% helix, 55% strand | P22629 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains B, C, A, D
- 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.72 | 0.78 | 88 | MPD |
| 2 | 424 | 0.64 | 0.78 | 44 | MPD |
| 3 | 312 | 0.62 | 0.79 | 43 | MRD |
Interfaces
6 interfaces between chains.
- C–D · 1641 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1617 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 423 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 398 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 197 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1N9Y · Streptavidin Mutant S27A at 1.5A 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 1N9Y · PDBe 1N9Y · UniProt P22629
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