MolNFT v1 · #92943 · protein
Crystal structure of beta-hexosaminidase 1 from burkholderia cenocepacia J2315 with bound N-acetyl-D-glucosamine
4GNV: “Crystal structure of beta-hexosaminidase 1 from burkholderia cenocepacia J2315 with bound…”. X-ray diffraction, 2 ligands (NAG, CL), 6 pockets (best druggability 0.71). MolNFT v1 #92943 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4GNV
- Type
- protein
- Length
- 680 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase 1
- EC
- 3.2.1.52
- UniProt
- B4EA43
- Ligands
- NAG, CL
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase 1 (EC 3.2.1.52) | protein | 337 | 46% helix, 12% strand | B4EA43 |
| B | Beta-hexosaminidase 1 (EC 3.2.1.52) | protein | 343 | 45% helix, 11% strand | B4EA43 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.71 | 0.85 | 45 | empty |
| 2 | 262 | 0.70 | 0.85 | 41 | CL |
| 3 | 121 | 0.57 | 0.84 | 23 | NAG |
| 4 | 124 | 0.57 | 0.83 | 24 | NAG |
| 5 | 52 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1613 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4GNV · Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315 with 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 B4EA43
- Elsewhere: RCSB PDB 4GNV · PDBe 4GNV · UniProt B4EA43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.