MolNFT v1 · #113219 · protein
Crystal structure beta-glucanase SDGLUC5_26A from saccharophagus degradans in complex with tetrasaccharide B
5A8P · Putative retaining B-glycosidase: “Crystal structure beta-glucanase SDGLUC5_26A from saccharophagus degradans in complex with tetrasaccharide B”. X-ray diffraction, 4 ligands (BGC, MG, SO4), 2 pockets (best druggability 0.49).…
- PDB
- 5A8P
- Type
- protein
- Length
- 336 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative retaining B-glycosidase
- EC
- 3.2.1.73
- UniProt
- Q21KE5
- Ligands
- BGC, MG, SO4, CL
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative retaining B-glycosidase (EC 3.2.1.73) | protein | 336 | 39% helix, 17% strand | Q21KE5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- PGE · Triethylene glycol · additive · 6 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
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 | 165 | 0.49 | 0.77 | 23 | BGC |
| 2 | 78 | 0.30 | 0.72 | 16 | empty |
Compared structures
- 5A8P · Crystal structure beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex… · 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 Q21KE5
- Elsewhere: RCSB PDB 5A8P · PDBe 5A8P · UniProt Q21KE5
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