MolNFT v1 · #140145 · protein
Crystal structure of insect beta-N-acetyl-D-hexosaminidase OFHEX1 complexed with a berberine derivative (sysu-00679)
5Y1B · Beta-hexosaminidase: “Crystal structure of insect beta-N-acetyl-D-hexosaminidase OFHEX1 complexed with a berberine derivative…”. X-ray diffraction, 2 ligands (8KL, NAG), 3 pockets (best druggability 0.65). MolNFT v1 #140145 on…
- PDB
- 5Y1B
- Type
- protein
- Length
- 572 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q06GJ0
- Ligands
- 8KL, NAG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 572 | 34% helix, 21% strand | Q06GJ0 |
Ligands and binding sites
- 8KL · 9-O-3'-quinolinium propylberberine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.65 | 0.81 | 44 | 8KL |
| 2 | 114 | 0.55 | 0.83 | 16 | empty |
| 3 | 175 | 0.54 | 0.80 | 25 | empty |
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5Y1B · Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06GJ0 · AlphaFold monomer V2.0 prediction for chitooligosaccharidolytic beta… · a predicted model of the same protein · 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 Q06GJ0
- Elsewhere: RCSB PDB 5Y1B · PDBe 5Y1B · UniProt Q06GJ0
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