MolNFT v1 · #119283 · protein
Characterization of a novel cbm from clostridium perfringens
5FRE · Exo-alpha-sialidase: “Characterization of a novel cbm from clostridium perfringens”. X-ray diffraction, 4 ligands (1PG, GAL, SIA), 3 pockets (best druggability 0.45). MolNFT v1 #119283 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5FRE
- Type
- protein
- Length
- 578 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-alpha-sialidase
- UniProt
- A0A0H2YQR1
- Ligands
- 1PG, GAL, SIA, CA
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-alpha-sialidase | protein | 194 | 10% helix, 44% strand | A0A0H2YQR1 |
| B | Exo-alpha-sialidase | protein | 193 | 11% helix, 45% strand | A0A0H2YQR1 |
| C | Exo-alpha-sialidase | protein | 191 | 11% helix, 44% strand | A0A0H2YQR1 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A, B, C
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 8 copies · chains A, B, C
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.45 | 0.76 | 22 | 1PG |
| 2 | 218 | 0.44 | 0.73 | 32 | empty |
| 3 | 104 | 0.37 | 0.75 | 21 | empty |
Interfaces
2 interfaces between chains.
- B–C · 629 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 188 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5FRE · Characterization of a novel CBM from Clostridium perfringens · 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 5FRE · PDBe 5FRE · UniProt A0A0H2YQR1
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