MolNFT v1 · #164595 · protein
Streptavidin variants harbouring an artificial organocatalyst based cofactor
6T2Y: “Streptavidin variants harbouring an artificial organocatalyst based cofactor”. X-ray diffraction, 1 ligand (HL9), 4 pockets (best druggability 0.47). MolNFT v1 #164595 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6T2Y
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- HL9
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 123 | 6% helix, 54% strand | P22629 |
| B | Streptavidin | protein | 121 | 2% helix, 55% strand | P22629 |
Ligands and binding sites
- HL9 · 5-[(3~{A}~{S},4~{S},6~{A}~{R})-2-oxidanylidene-1,3, 3~{A},4,6,6~{A}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.47 | 0.78 | 22 | HL9 |
| 2 | 103 | 0.47 | 0.80 | 22 | HL9 |
| 3 | 68 | 0.33 | 0.76 | 18 | EDO |
| 4 | 66 | 0.29 | 0.74 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 1542 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6T2Y · Streptavidin variants harbouring an artificial organocatalyst based cofactor · 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 6T2Y · PDBe 6T2Y · UniProt P22629
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