Research workbench
Streptavidin variants harbouring an artificial organocatalyst based cofactor
Analyse Streptavidin variants harbouring an artificial organocatalyst based cofactor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T1G
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptavidin
- UniProt
- P22629
- Ligands
- HL9
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Streptavidin | protein | 133 | 9% helix, 48% strand | P22629 |
| B | Streptavidin | protein | 123 | 6% helix, 54% 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 · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.46 | 0.78 | 26 | HL9 |
| 2 | 103 | 0.46 | 0.79 | 20 | HL9 |
Interfaces
1 interface between chains.
- A–B · 222 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6T1G · Streptavidin variants harbouring an artificial organocatalyst based cofactor · 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 6T1G · PDBe 6T1G · UniProt P22629
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