Research workbench
Chimeric Streptavidin With A Dimerization Domain For Artificial Transfer Hydrogenation
Analyse Chimeric Streptavidin With A Dimerization Domain For Artificial Transfer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B74
- Type
- protein
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97); Streptomyces avidinii
- Molecule
- Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin
- EC
- 1.15.1.1
- UniProt
- P22629, P0A609
- Ligands
- 4IR
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.85 · 3 distinct chains · 8% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA, DDD | Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin (EC 1.15.1.1) | protein | 122 | 8% helix, 55% strand | P22629, P0A609 |
| BBB | Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin (EC 1.15.1.1) | protein | 125 | 8% helix, 54% strand | P22629, P0A609 |
| CCC | Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin (EC 1.15.1.1) | protein | 123 | 8% helix, 54% strand | P22629, P0A609 |
Ligands and binding sites
- 4IR · {N-(4-{[2-(amino-kappaN)ethyl]sulfamoyl-kappaN}phenyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}(chloro)[(1,2,3,4,5-eta)-1,2,3,4,5-pentamethylcyclopentadienyl]iridium(III) · ligand · 4 copies · chains AAA, BBB, CCC, DDD
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.66 | 0.80 | 56 | empty |
| 2 | 193 | 0.58 | 0.81 | 27 | empty |
| 3 | 110 | 0.56 | 0.84 | 26 | 4IR |
| 4 | 91 | 0.55 | 0.85 | 24 | 4IR |
| 5 | 106 | 0.55 | 0.83 | 24 | 4IR |
Interfaces
6 interfaces between chains.
- AAA–CCC · 1631 Ų buried · 28 hydrogen bonds · protein-protein
- BBB–DDD · 1622 Ų buried · 28 hydrogen bonds · protein-protein
- AAA–BBB · 547 Ų buried · 3 hydrogen bonds · protein-protein
- CCC–DDD · 541 Ų buried · 2 hydrogen bonds · protein-protein
- AAA–DDD · 222 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- P0A609 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (P0A609) · a predicted model of the same protein · chain CCC against A, TM-score 0.41
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
- Every structure of UniProt P0A609
- Elsewhere: RCSB PDB 7B74 · PDBe 7B74 · UniProt P22629 · UniProt P0A609
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