MolNFT v1 · #113216 · protein
Crystal structure of the selenomethionine derivative of beta-glucanase SDGLUC5_26A from saccharophagus degradans
5A8M · Putative retaining B-glycosidase: “Crystal structure of the selenomethionine derivative of beta-glucanase SDGLUC5_26A from saccharophagus…”. X-ray diffraction, 3 ligands (MG, CL, SO4), 11 pockets (best druggability 0.62). MolNFT v1…
- PDB
- 5A8M
- Type
- protein
- Length
- 1,011 residues
- Chains
- 3
- 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
- MG, CL, SO4
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative retaining B-glycosidase (EC 3.2.1.73) | protein | 337 | 40% helix, 17% strand | Q21KE5 |
| B | Putative retaining B-glycosidase (EC 3.2.1.73) | protein | 337 | 40% helix, 17% strand | Q21KE5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 9 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 22 copies · chains A, B, C
- GOL · Glycerol · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.62 | 0.79 | 28 | GOL, PGE |
| 2 | 273 | 0.62 | 0.80 | 27 | GOL, PGE |
| 3 | 280 | 0.62 | 0.80 | 30 | GOL, PGE |
| 4 | 250 | 0.58 | 0.79 | 34 | GOL |
| 5 | 244 | 0.57 | 0.78 | 33 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 959 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 957 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 952 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 5A8M · Crystal structure of the selenomethionine derivative of beta-glucanase SdGluc5_26A from… · 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 5A8M · PDBe 5A8M · UniProt Q21KE5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.