Research workbench
The crystal structure of beta-hexosaminidase B in complex with pyrimethamine
Analyse The crystal structure of beta-hexosaminidase B in complex with pyrimethamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LMY
- Type
- protein
- Length
- 959 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase subunit beta
- EC
- 3.2.1.52
- UniProt
- P07686
- Ligands
- CP6, NAG, NDG, BMA, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase subunit beta (EC 3.2.1.52) | protein | 479 | 37% helix, 21% strand | P07686 |
| B | Beta-hexosaminidase subunit beta (EC 3.2.1.52) | protein | 480 | 36% helix, 21% strand | P07686 |
Ligands and binding sites
- CP6 · 5-(4-chloro-phenyl)-6-ethyl-pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.70 | 0.76 | 66 | empty |
| 2 | 232 | 0.65 | 0.83 | 30 | empty |
| 3 | 189 | 0.52 | 0.77 | 19 | empty |
| 4 | 201 | 0.51 | 0.77 | 22 | empty |
| 5 | 51 | 0.38 | 0.80 | 14 | CP6 |
Interfaces
1 interface between chains.
- A–B · 835 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 3LMY · The Crystal Structure of beta-hexosaminidase B in complex with Pyrimethamine · the same entry in another collection · chain A against A, TM-score 1.00
- P07686 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase subunit beta (P07686) · 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 P07686
- Elsewhere: RCSB PDB 3LMY · PDBe 3LMY · UniProt P07686
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