Research workbench
Crystal structure of burkholderia cenocepacia family 3 glycoside hydrolase (nagz) bound to (3S,4R,5R,6S)-3-butyryl-4,5,6- trihydroxyazepane
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
- 5UTR
- Type
- protein
- Length
- 679 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
- 8MP
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 339 | 45% helix, 12% strand | A0A125HFC0 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 340 | 46% helix, 12% strand | A0A125HFC0 |
Ligands and binding sites
- 8MP · N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]butanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.73 | 0.87 | 47 | empty |
| 2 | 292 | 0.71 | 0.85 | 44 | empty |
| 3 | 128 | 0.61 | 0.85 | 24 | 8MP |
| 4 | 143 | 0.60 | 0.84 | 24 | 8MP |
| 5 | 50 | 0.32 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1735 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5UTR · 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 5UTR · PDBe 5UTR · UniProt A0A125HFC0
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