MolNFT v1 · #38021 · protein
Crystallographic structure of human beta-hexosaminidase a
2GJX · Beta-hexosaminidase alpha chain: “Crystallographic structure of human beta-hexosaminidase a”. X-ray diffraction, 3 ligands (NAG, BMA, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #38021 on GenesisL1: 3D structure, binding…
- PDB
- 2GJX
- Type
- protein
- Length
- 3,889 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase alpha chain; Beta-hexosaminidase beta chain
- EC
- 3.2.1.52
- UniProt
- P06865, P07686
- Ligands
- NAG, BMA, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, H | Beta-hexosaminidase alpha chain (EC 3.2.1.52) | protein | 492 | 34% helix, 20% strand | P06865 |
| B, F, G | Beta-hexosaminidase beta chain (EC 3.2.1.52) | protein | 480 | 35% helix, 20% strand | P07686 |
| C | Beta-hexosaminidase beta chain (EC 3.2.1.52) | protein | 481 | 35% helix, 20% strand | P07686 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B, C, D, E, G, H, F
- BMA · beta-D-mannopyranose · sugar · 4 copies
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.81 | 0.98 | 34 | empty |
| 2 | 122 | 0.80 | 0.98 | 34 | empty |
| 3 | 126 | 0.79 | 0.98 | 35 | empty |
| 4 | 117 | 0.79 | 0.97 | 38 | empty |
| 5 | 922 | 0.77 | 0.80 | 101 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1623 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1614 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1605 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1589 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1014 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 2GJX · Crystallographic structure of human beta-Hexosaminidase A · the same entry in another collection · chain H against H, TM-score 1.00
- P06865 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase subunit alpha (P06865) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P07686 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase subunit beta (P07686) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P06865
- Every structure of UniProt P07686
- Elsewhere: RCSB PDB 2GJX · PDBe 2GJX · UniProt P06865 · UniProt P07686
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