Research workbench
Crystal structure of beta-glucanase SDGLUC5_26A from saccharophagus degradans in complex with tetrasaccharide a, form 2
Analyse Crystal structure of beta-glucanase SDGLUC5_26A from saccharophagus degradans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A95
- Type
- protein
- Length
- 1,008 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
- BGC, MG, NA, CL
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative retaining B-glycosidase (EC 3.2.1.73) | protein | 337 | 40% helix, 16% strand | Q21KE5 |
| B | Putative retaining B-glycosidase (EC 3.2.1.73) | protein | 335 | 40% helix, 16% strand | Q21KE5 |
| C | Putative retaining B-glycosidase (EC 3.2.1.73) | protein | 336 | 40% helix, 16% strand | Q21KE5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 9 copies · chains A, C, B
- MG · Magnesium ion · metal · 5 copies · chains A, B, C
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 12 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.71 | 0.76 | 83 | empty |
| 2 | 295 | 0.61 | 0.79 | 32 | BGC |
| 3 | 268 | 0.61 | 0.79 | 29 | BGC |
| 4 | 293 | 0.60 | 0.78 | 29 | BGC |
| 5 | 181 | 0.53 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 956 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 925 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 870 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5A95 · Crystal structure of 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 5A95 · PDBe 5A95 · UniProt Q21KE5
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