Research workbench
Crystal structure of mshb with glycerol and acetate bound in the active site
Analyse Crystal structure of mshb with glycerol and acetate bound in the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EWL
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase
- EC
- 3.5.1.103
- UniProt
- O50426
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase (EC 3.5.1.103) | protein | 299 | 33% helix, 18% strand | O50426 |
| B | 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase (EC 3.5.1.103) | protein | 290 | 34% helix, 17% strand | O50426 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.80 | 0.84 | 60 | ACT, GOL |
| 2 | 869 | 0.78 | 0.81 | 82 | ACT, GOL |
| 3 | 92 | 0.33 | 0.73 | 23 | PE4 |
Interfaces
1 interface between chains.
- A–B · 857 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4EWL · Crystal Structure of MshB with glycerol and Acetate bound in the active site · 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 O50426
- Elsewhere: RCSB PDB 4EWL · PDBe 4EWL · UniProt O50426
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