Research workbench
Crystal structure of a rice OS3BGLU6 beta-glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396
Analyse Crystal structure of a rice OS3BGLU6 beta-glucosidase with covalently bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GNR
- Type
- protein
- Length
- 478 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OS03G0212800 protein
- EC
- 3.2.1.21
- UniProt
- Q8L7J2
- Ligands
- G2F
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OS03G0212800 protein (EC 3.2.1.21) | protein | 478 | 44% helix, 17% strand | Q8L7J2 |
Ligands and binding sites
- G2F · 2-deoxy-2-fluoro-alpha-D-glucopyranose · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.73 | 0.81 | 53 | G2F |
| 2 | 95 | 0.38 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 3GNR · Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8L7J2 · AlphaFold monomer V2.0 prediction for beta-glucosidase 6 (Q8L7J2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8L7J2
- Elsewhere: RCSB PDB 3GNR · PDBe 3GNR · UniProt Q8L7J2
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