MolNFT v1 · #65120 · protein
Crystal structure of a rice OS3BGLU6 beta-glucosidase with octyl-beta- D-thio-glucoside
3GNP · OS03G0212800 protein: “Crystal structure of a rice OS3BGLU6 beta-glucosidase with octyl-beta- D-thio-glucoside”. X-ray diffraction, 1 ligand (SOG), 3 pockets (best druggability 0.75). MolNFT v1 #65120 on GenesisL1: 3D structure…
- PDB
- 3GNP
- 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
- SOG
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OS03G0212800 protein (EC 3.2.1.21) | protein | 478 | 45% helix, 17% strand | Q8L7J2 |
Ligands and binding sites
- SOG · octyl 1-thio-beta-D-glucopyranoside · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.75 | 0.81 | 51 | SOG, GOL |
| 2 | 79 | 0.36 | 0.76 | 27 | GOL |
| 3 | 102 | 0.36 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3GNP · Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with Octyl-Beta-D-Thio-Glucoside · 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 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 Q8L7J2
- Elsewhere: RCSB PDB 3GNP · PDBe 3GNP · UniProt Q8L7J2
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