MolNFT v1 · #5009 · protein
Crystal structure of the inactive mutant monocot (maize ZMGLU1) beta- glucosidase ZMGLUE191D in complex with the natural substrate dimboa- beta-D-glucoside
1E56 · Beta-glucosidase: “Crystal structure of the inactive mutant monocot (maize ZMGLU1) beta- glucosidase ZMGLUE191D in complex with…”. X-ray diffraction, 2 ligands (HBO, BGC), 7 pockets (best druggability 0.74). MolNFT v1 #5009 on…
- PDB
- 1E56
- Type
- protein
- Length
- 978 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- P49235
- Ligands
- HBO, BGC
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucosidase (EC 3.2.1.21) | protein | 489 | 42% helix, 18% strand | P49235 |
Ligands and binding sites
- HBO · 2,4-dihydroxy-7-(methyloxy)-2H-1,4-benzoxazin-3(4H)-one · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.74 | 0.83 | 42 | BGC, HBO |
| 2 | 449 | 0.73 | 0.83 | 43 | BGC, HBO |
| 3 | 387 | 0.71 | 0.83 | 41 | empty |
| 4 | 68 | 0.36 | 0.77 | 15 | empty |
| 5 | 56 | 0.35 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, glycosylation).
Compared structures
- 1E56 · Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) beta-glucosidase… · the same entry in another collection · chain A against A, TM-score 1.00
- P49235 · AlphaFold monomer V2.0 prediction for 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxa… · 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 P49235
- Elsewhere: RCSB PDB 1E56 · PDBe 1E56 · UniProt P49235
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