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Different transition state conformations for the hydrolysis of beta-mannosides and beta-glucosides in the rice Os7BGlu26 family GH1 beta-mannosidase/beta-glucosidase
Analyse Different transition state conformations for the hydrolysis of beta-mannosides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RE3
- Type
- protein
- Length
- 483 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Oryza sativa Indica Group
- Molecule
- Beta-mannosidase/beta-glucosidase
- EC
- 3.2.1.25
- UniProt
- B5ABY0
- Ligands
- GIM
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.55 · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase/beta-glucosidase (EC 3.2.1.25) | protein | 483 | 45% helix, 16% strand | B5ABY0 |
Ligands and binding sites
- GIM · Glucoimidazole · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.77 | 0.86 | 39 | EPE, GOL, GIM |
| 2 | 59 | 0.28 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4RE3 · Different transition state conformations for the hydrolysis of beta- mannosides and… · the same entry in another collection · 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 B5ABY0
- Elsewhere: RCSB PDB 4RE3 · PDBe 4RE3 · UniProt B5ABY0
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