Research workbench
Streptavidin mutant Y43A at 1.70A resolution
Analyse Streptavidin mutant Y43A at 1.70A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NBX
- Type
- protein
- Length
- 467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 120 | 5% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 118 | 5% helix, 57% strand | P22629 |
| C | Streptavidin | protein | 113 | 5% helix, 59% strand | P22629 |
| D | Streptavidin | protein | 116 | 5% helix, 59% strand | P22629 |
Ligands and binding sites
- 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.62 | 0.84 | 28 | MRD |
| 2 | 322 | 0.62 | 0.79 | 38 | empty |
| 3 | 329 | 0.61 | 0.78 | 41 | empty |
| 4 | 325 | 0.61 | 0.78 | 41 | empty |
| 5 | 170 | 0.54 | 0.80 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1656 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1603 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 399 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 206 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1NBX · Streptavidin Mutant Y43A at 1.70A 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 1NBX · PDBe 1NBX · UniProt P22629
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