Research workbench
Crystal structure of rice BGLU1 E176Q mutant in complex with laminaribiose
Analyse Crystal structure of rice BGLU1 E176Q mutant in complex with laminaribiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AHT
- Type
- protein
- Length
- 942 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase 7
- EC
- 3.2.1.21
- UniProt
- Q75I93
- Ligands
- BGC, ZN, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucosidase 7 (EC 3.2.1.21) | protein | 471 | 44% helix, 16% strand | Q75I93 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 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
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 | 443 | 0.69 | 0.80 | 41 | BGC |
| 2 | 480 | 0.68 | 0.79 | 40 | BGC |
| 3 | 326 | 0.57 | 0.76 | 33 | empty |
| 4 | 325 | 0.57 | 0.76 | 37 | empty |
| 5 | 56 | 0.38 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 586 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3AHT · Crystal structure of rice BGlu1 E176Q mutant in complex with laminaribiose · the same entry in another collection · chain A against A, TM-score 1.00
- Q75I93 · AlphaFold monomer V2.0 prediction for beta-glucosidase 7 (Q75I93) · 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 Q75I93
- Elsewhere: RCSB PDB 3AHT · PDBe 3AHT · UniProt Q75I93
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