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Crystal structure of insect beta-N-acetyl-D-hexosaminidase OFHEX1 complexed with naphthalimide derivative Q2
Analyse Crystal structure of insect beta-N-acetyl-D-hexosaminidase OFHEX1 complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WMC
- 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
- NF6, NAG
- Pockets
- 5 · best druggability 0.58
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
- NF6 · 6-(dimethylamino)-2-(2-{[(5-methyl-1,3,4-thiadiazol-2-yl)methyl]amino}ethyl)-1H-benzo[de]isoquinoline-1,3(2H)-dione · 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.58 | 0.84 | 29 | empty |
| 2 | 187 | 0.54 | 0.79 | 26 | empty |
| 3 | 105 | 0.52 | 0.82 | 12 | empty |
| 4 | 69 | 0.29 | 0.73 | 16 | empty |
| 5 | 59 | 0.28 | 0.73 | 18 | empty |
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3WMC · Crystal structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with… · 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 3WMC · PDBe 3WMC · UniProt Q06GJ0
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