Research workbench
Human lysosomal beta-hexosaminidase isoform B in complex with intermediate analogue nag-thiazoline
Analyse Human lysosomal beta-hexosaminidase isoform B in complex with intermediate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NP0
- Type
- protein
- Length
- 960 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase subunit beta; Beta-hexosaminidase subunit beta chain B…
- EC
- 3.2.1.52
- UniProt
- P07686
- Ligands
- NGT, NAG, SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-hexosaminidase subunit beta | protein | 53 | 34% helix, 26% strand | P07686 |
| C, E | Beta-hexosaminidase subunit beta chain B (EC 3.2.1.52) | protein | 190 | 26% helix, 29% strand | P07686 |
| D, F | Beta-hexosaminidase subunit beta chain a (EC 3.2.1.52) | protein | 237 | 43% helix, 13% strand | P07686 |
Ligands and binding sites
- NGT · 3ar,5r,6s,7r,7ar-5-hydroxymethyl-2-methyl-5,6,7,7A-tetrahydro-3AH-pyrano[3,2-d]thiazole-6,7-diol · ligand · 2 copies · chains C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B, E
- SO4 · Sulfate ion · ion · chains F
- GOL · Glycerol · additive · 3 copies · chains C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.63 | 0.74 | 44 | empty |
| 2 | 213 | 0.63 | 0.83 | 28 | empty |
| 3 | 209 | 0.62 | 0.82 | 22 | empty |
| 4 | 207 | 0.49 | 0.76 | 28 | empty |
| 5 | 176 | 0.49 | 0.77 | 22 | empty |
Interfaces
9 interfaces between chains.
- E–F · 3375 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3347 Ų buried · 55 hydrogen bonds · protein-protein
- B–E · 2109 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2105 Ų buried · 38 hydrogen bonds · protein-protein
- B–F · 567 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1NP0 · Human lysosomal beta-hexosaminidase isoform B in complex with intermediate analogue… · the same entry in another collection · chain F against F, TM-score 1.00
- P07686 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase subunit beta (P07686) · a predicted model of the same protein · chain C 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 P07686
- Elsewhere: RCSB PDB 1NP0 · PDBe 1NP0 · UniProt P07686
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