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Crystal structure of oryza sativa OS4BGLU18 monolignol beta- glucosidase with delta-gluconolactone
Analyse Crystal structure of oryza sativa OS4BGLU18 monolignol beta- glucosidase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D6B
- Type
- protein
- Length
- 952 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase 18
- EC
- 3.2.1.21
- UniProt
- Q7XSK0
- Ligands
- LGC, ZN
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase 18 (EC 3.2.1.21) | protein | 475 | 43% helix, 17% strand | Q7XSK0 |
| B | Beta-glucosidase 18 (EC 3.2.1.21) | protein | 477 | 44% helix, 17% strand | Q7XSK0 |
Ligands and binding sites
- LGC · D-glucono-1,5-lactone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A, B
- GOL · Glycerol · additive · 16 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.72 | 0.82 | 49 | LGC, GOL |
| 2 | 112 | 0.72 | 0.92 | 29 | GOL |
| 3 | 367 | 0.70 | 0.82 | 37 | LGC, GOL |
| 4 | 112 | 0.69 | 0.91 | 29 | GOL |
| 5 | 437 | 0.65 | 0.78 | 53 | GOL |
Interfaces
1 interface between chains.
- A–B · 407 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7D6B · Crystal structure of Oryza sativa Os4BGlu18 monolignol beta-glucosidase with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7XSK0 · AlphaFold monomer V2.0 prediction for beta-glucosidase 18 (Q7XSK0) · 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 Q7XSK0
- Elsewhere: RCSB PDB 7D6B · PDBe 7D6B · UniProt Q7XSK0
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