MolNFT v1 · #115319 · protein
Crystal structure of spodoptera frugiperda beta-glycosidase
5CG0 · Beta-glucosidase: “Crystal structure of spodoptera frugiperda beta-glycosidase”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.70). MolNFT v1 #115319 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CG0
- Type
- protein
- Length
- 2,906 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- UniProt
- O61594
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-glucosidase | protein | 488 | 42% helix, 15% strand | O61594 |
| D | Beta-glucosidase | protein | 486 | 42% helix, 16% strand | O61594 |
| E | Beta-glucosidase | protein | 485 | 42% helix, 15% strand | O61594 |
| F | Beta-glucosidase | protein | 471 | 43% helix, 16% strand | O61594 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, D, C, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.70 | 0.75 | 85 | empty |
| 2 | 312 | 0.69 | 0.83 | 37 | TRS |
| 3 | 238 | 0.67 | 0.84 | 30 | TRS |
| 4 | 341 | 0.66 | 0.81 | 38 | TRS |
| 5 | 477 | 0.65 | 0.77 | 56 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1001 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 941 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 925 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 662 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 340 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5CG0 · Crystal structure of Spodoptera frugiperda Beta-glycosidase · 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 O61594
- Elsewhere: RCSB PDB 5CG0 · PDBe 5CG0 · UniProt O61594
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