Research workbench
Crystal structure of burkholderia cenocepacia family 3 glycoside hydrolase (nagz) bound to N-ethylbutyryl-pugnac
Analyse Crystal structure of burkholderia cenocepacia family 3 glycoside hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UTP
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- A0A125HFC0
- Ligands
- 8M7
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 331 | 47% helix, 11% strand | A0A125HFC0 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 335 | 47% helix, 12% strand | A0A125HFC0 |
Ligands and binding sites
- 8M7 · N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]-2-ethylbutanamide · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.74 | 0.86 | 46 | empty |
| 2 | 272 | 0.72 | 0.86 | 43 | empty |
| 3 | 176 | 0.49 | 0.77 | 29 | 8M7 |
| 4 | 160 | 0.48 | 0.76 | 26 | 8M7 |
| 5 | 86 | 0.40 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1674 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5UTP · Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound… · 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 A0A125HFC0
- Elsewhere: RCSB PDB 5UTP · PDBe 5UTP · UniProt A0A125HFC0
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