MolNFT v1 · #50381 · protein
Rice BGLU1 beta-glucosidase, a plant EXOGLUCANASE/BETA-glucosidase
2RGM: “Rice BGLU1 beta-glucosidase, a plant EXOGLUCANASE/BETA-glucosidase”. X-ray diffraction, 3 ligands (G2F, ZN, SO4), 6 pockets (best druggability 0.68). MolNFT v1 #50381 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2RGM
- Type
- protein
- Length
- 942 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- Q42975
- Ligands
- G2F, ZN, SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucosidase (EC 3.2.1.21) | protein | 471 | 45% helix, 16% strand | Q42975 |
Ligands and binding sites
- G2F · 2-deoxy-2-fluoro-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.68 | 0.81 | 37 | G2F, GOL |
| 2 | 389 | 0.68 | 0.80 | 38 | G2F, GOL |
| 3 | 318 | 0.56 | 0.76 | 33 | empty |
| 4 | 328 | 0.56 | 0.75 | 33 | empty |
| 5 | 63 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 610 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 2RGM · Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase · 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 Q42975
- Elsewhere: RCSB PDB 2RGM · PDBe 2RGM · UniProt Q42975
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