MolNFT v1 · #163502 · protein
SCDSAV(SARK)MV2 - engineering single-chain dimeric streptavidin as host for artificial metalloenzymes
6S50: “SCDSAV(SARK)MV2 - engineering single-chain dimeric streptavidin as host for artificial metalloenzymes”. X-ray diffraction, 2 ligands (4IR, SO4), 5 pockets (best druggability 0.77). MolNFT v1 #163502 on GenesisL1: 3D structure…
- PDB
- 6S50
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- 4IR, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 248 | 8% helix, 55% strand | P22629 |
| B | Streptavidin | protein | 246 | 7% helix, 55% strand | P22629 |
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 A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 6 copies · chains A, 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 | 856 | 0.77 | 0.80 | 105 | 4IR |
| 2 | 92 | 0.61 | 0.88 | 21 | 4IR |
| 3 | 97 | 0.55 | 0.84 | 26 | 4IR |
| 4 | 162 | 0.54 | 0.80 | 28 | empty |
| 5 | 170 | 0.53 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1390 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6S50 · scdSav(SARK)mv2 - Engineering Single-Chain Dimeric Streptavidin as Host for Artificial… · the same entry in another collection · chain B against B, 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 6S50 · PDBe 6S50 · UniProt P22629
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