MolNFT v1 · #146812 · protein
Glcnac-inspired cyclophellitol bound to nagz
6DTE · Beta-hexosaminidase: “Glcnac-inspired cyclophellitol bound to nagz”. X-ray diffraction, 1 ligand (H9J), 4 pockets (best druggability 0.73). MolNFT v1 #146812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DTE
- 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
- H9J
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% 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 | 45% helix, 12% strand | A0A125HFC0 |
Ligands and binding sites
- H9J · 2,2,2-trifluoro-N-[(1R,2R,3R,4R,5R,6R)-2,3,5,6-tetrahydroxy-4-(hydroxymethyl)cyclohexyl]acetamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.73 | 0.86 | 44 | empty |
| 2 | 302 | 0.72 | 0.85 | 51 | empty |
| 3 | 104 | 0.56 | 0.85 | 25 | H9J |
| 4 | 112 | 0.55 | 0.83 | 24 | H9J |
Interfaces
1 interface between chains.
- A–B · 1688 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6DTE · GlcNAc-inspired cyclophellitol bound to NagZ · 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 6DTE · PDBe 6DTE · UniProt A0A125HFC0
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