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Crystal structure of insect beta-N-acetyl-D-hexosaminidase OFHEX1 E328A complexed with tmg-chitotriomycin
Analyse Crystal structure of insect beta-N-acetyl-D-hexosaminidase OFHEX1 E328A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VTR
- Type
- protein
- Length
- 572 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosaminidase
- EC
- 3.2.1.52
- UniProt
- Q06GJ0
- Ligands
- TMX, NAG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglucosaminidase (EC 3.2.1.52) | protein | 572 | 34% helix, 22% strand | Q06GJ0 |
Ligands and binding sites
- TMX · 2-deoxy-2-(trimethylammonio)-beta-D-glucopyranose · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.69 | 0.83 | 40 | NAG, TMX |
| 2 | 190 | 0.54 | 0.79 | 25 | empty |
| 3 | 86 | 0.48 | 0.82 | 20 | empty |
| 4 | 53 | 0.27 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3VTR · Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 E328A 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 3VTR · PDBe 3VTR · UniProt Q06GJ0
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