Research workbench
CBM40_CPF0721-6'SL
Analyse CBM40_CPF0721-6'SL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FRA
- Type
- protein
- Length
- 1,165 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase
- UniProt
- A0A0H2YQR1
- Ligands
- SIA, GAL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase | protein | 197 | 11% helix, 43% strand | A0A0H2YQR1 |
| B, C, D | Sialidase | protein | 194 | 11% helix, 45% strand | A0A0H2YQR1 |
| E, F | Sialidase | protein | 193 | 10% helix, 45% strand | A0A0H2YQR1 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, B, C, D, E, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains B
- ACT · Acetate ion · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.76 | 0.79 | 127 | empty |
| 2 | 892 | 0.75 | 0.79 | 94 | ACT |
| 3 | 106 | 0.52 | 0.82 | 22 | empty |
| 4 | 188 | 0.49 | 0.76 | 24 | empty |
| 5 | 155 | 0.40 | 0.73 | 27 | empty |
Interfaces
9 interfaces between chains.
- D–E · 644 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 577 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 382 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 380 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 327 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5FRA · CBM40_CPF0721-6'SL · 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 A0A0H2YQR1
- Elsewhere: RCSB PDB 5FRA · PDBe 5FRA · UniProt A0A0H2YQR1
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