MolNFT v1 · #120062 · protein
The M3 mutant structure of BGL6
5GNZ · Beta-glucosidase: “The M3 mutant structure of BGL6”. X-ray diffraction, 1 ligand (BGC), 20 pockets (best druggability 0.75). MolNFT v1 #120062 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GNZ
- Type
- protein
- Length
- 3,581 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- Ligands
- BGC
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, I | Beta-glucosidase (EC 3.2.1.21) | protein | 448 | 43% helix, 16% strand | — |
| C, H, K | Beta-glucosidase (EC 3.2.1.21) | protein | 447 | 43% helix, 16% strand | — |
| J | Beta-glucosidase (EC 3.2.1.21) | protein | 448 | 43% helix, 15% strand | — |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, H, I, J, K
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.75 | 0.80 | 73 | empty |
| 2 | 1063 | 0.75 | 0.77 | 88 | empty |
| 3 | 619 | 0.72 | 0.80 | 59 | empty |
| 4 | 607 | 0.71 | 0.79 | 62 | empty |
| 5 | 497 | 0.71 | 0.80 | 50 | BGC |
Interfaces
13 interfaces between chains.
- J–K · 1042 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1035 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 1031 Ų buried · 12 hydrogen bonds · protein-protein
- H–J · 567 Ų buried · 4 hydrogen bonds · protein-protein
- I–K · 566 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5GNZ · The M3 mutant structure of Bgl6 · 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 5GNZ · PDBe 5GNZ
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