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Crystal structure of the inactive mutant monocot (maize ZMGLU1) beta- glucosidase ZMGLUE191D in complex with the competitive inhibitor dhurrin
Analyse Crystal structure of the inactive mutant monocot (maize ZMGLU1) beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E55
- Type
- protein
- Length
- 982 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
- DHR, BGC
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 492 | 42% helix, 18% strand | P49235 |
| B | Beta-glucosidase (EC 3.2.1.21) | protein | 490 | 42% helix, 18% strand | P49235 |
Ligands and binding sites
- DHR · (2S)-hydroxy(4-hydroxyphenyl)ethanenitrile · 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 | 413 | 0.73 | 0.83 | 42 | BGC, DHR |
| 2 | 425 | 0.72 | 0.83 | 43 | BGC, DHR |
| 3 | 368 | 0.71 | 0.83 | 34 | empty |
| 4 | 66 | 0.36 | 0.77 | 17 | empty |
| 5 | 72 | 0.36 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1079 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1E55 · 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 B 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 1E55 · PDBe 1E55 · UniProt P49235
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