Research workbench
Crystal structure of beta-glucosidase bglm-G1 from marine metagenome
Analyse Crystal structure of beta-glucosidase bglm-G1 from marine metagenome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NS6
- Type
- protein
- Length
- 1,314 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-glucosidase (EC 3.2.1.21) | protein | 438 | 44% helix, 17% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, C, B
- GOL · Glycerol · additive · 23 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.86 | 0.87 | 111 | GOL |
| 2 | 539 | 0.72 | 0.81 | 63 | SO4, GOL |
| 3 | 474 | 0.71 | 0.81 | 58 | SO4, GOL |
| 4 | 419 | 0.70 | 0.81 | 45 | GOL |
| 5 | 402 | 0.69 | 0.81 | 45 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 969 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 960 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 953 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5NS6 · Crystal structure of beta-glucosidase BglM-G1 from marine metagenome · 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 5NS6 · PDBe 5NS6
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