Research workbench
Human beta-glucuronidase at 1.7 a resolution
Analyse Human beta-glucuronidase at 1.7 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HN3
- Type
- protein
- Length
- 2,430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- P08236
- Ligands
- GUP, MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase (EC 3.2.1.31) | protein | 608 | 23% helix, 33% strand | P08236 |
| B | Beta-glucuronidase (EC 3.2.1.31) | protein | 609 | 23% helix, 33% strand | P08236 |
| D | Beta-glucuronidase (EC 3.2.1.31) | protein | 607 | 23% helix, 33% strand | P08236 |
| E | Beta-glucuronidase (EC 3.2.1.31) | protein | 606 | 22% helix, 33% strand | P08236 |
Ligands and binding sites
- GUP · alpha-L-gulopyranose · ligand
- MAN · alpha-D-mannopyranose · sugar · 26 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, D, E
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, D, E
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains A, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, E
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 | 1056 | 0.89 | 0.90 | 93 | empty |
| 2 | 854 | 0.86 | 0.88 | 111 | empty |
| 3 | 782 | 0.85 | 0.88 | 87 | empty |
| 4 | 86 | 0.78 | 0.99 | 20 | empty |
| 5 | 89 | 0.77 | 0.98 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2037 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1986 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1930 Ų buried · 31 hydrogen bonds · protein-protein
- B–E · 1909 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 656 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan (N-glycosylation).
Compared structures
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 P08236
- Elsewhere: RCSB PDB 3HN3 · PDBe 3HN3 · UniProt P08236
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