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Structural insight into the beta-GH1 glucosidase BGLN1 from oleaginous microalgae nannochloropsis
Analyse Structural insight into the beta-GH1 glucosidase BGLN1 from oleaginous… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YJ7
- Type
- protein
- Length
- 1,944 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- EC
- 3.2.1.21
- Ligands
- CA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glycoside hydrolase (EC 3.2.1.21) | protein | 483 | 46% helix, 15% strand | — |
| B | Glycoside hydrolase (EC 3.2.1.21) | protein | 488 | 45% helix, 15% strand | — |
| C | Glycoside hydrolase (EC 3.2.1.21) | protein | 490 | 46% helix, 15% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.77 | 0.82 | 62 | GOL |
| 2 | 640 | 0.71 | 0.78 | 58 | GOL |
| 3 | 335 | 0.71 | 0.83 | 34 | GOL |
| 4 | 320 | 0.70 | 0.83 | 35 | GOL |
| 5 | 690 | 0.69 | 0.77 | 63 | empty |
Interfaces
5 interfaces between chains.
- A–C · 563 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 350 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 183 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 92 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5YJ7 · Structural insight into the beta-GH1 glucosidase BGLN1 from oleaginous microalgae… · 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
- Elsewhere: RCSB PDB 5YJ7 · PDBe 5YJ7
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