Research workbench
Sialidase26 co-crystallized with DANA-Gc
Analyse Sialidase26 co-crystallized with DANA-Gc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MYV
- Type
- protein
- Length
- 2,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- unidentified bacterium
- Molecule
- Sialidase26
- Ligands
- GC9
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Sialidase26 | protein | 522 | 6% helix, 46% strand | — |
| C | Sialidase26 | protein | 526 | 6% helix, 46% strand | — |
Ligands and binding sites
- GC9 · 2,6-anhydro-3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-L-altro-non-2-enonic acid · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.71 | 0.79 | 56 | GC9 |
| 2 | 322 | 0.69 | 0.83 | 27 | empty |
| 3 | 598 | 0.66 | 0.76 | 58 | empty |
| 4 | 345 | 0.66 | 0.81 | 29 | empty |
| 5 | 307 | 0.64 | 0.80 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1625 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 425 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 276 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 193 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MYV · SIALIDASE26 co-crystallized with dana-gc · 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
- Elsewhere: RCSB PDB 6MYV · PDBe 6MYV
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