MolNFT v1 · #185417 · protein
Crystal structure of endoglycosidase E GH18 domain from enterococcus faecalis in complex with MAN5 product
7PUK · Beta-N-acetylhexosaminidase: “Crystal structure of endoglycosidase E GH18 domain from enterococcus faecalis in complex with MAN5 product”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 7 pockets (best druggability 0.52). MolNFT v1…
- PDB
- 7PUK
- Type
- protein
- Length
- 847 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylhexosaminidase
- EC
- 3.2.1.52
- UniProt
- Q6U890
- Ligands
- MAN, NAG, BMA
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 425 | 51% helix, 11% strand | Q6U890 |
| C | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 422 | 50% helix, 11% strand | Q6U890 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.52 | 0.73 | 47 | NAG, BMA, MAN |
| 2 | 59 | 0.45 | 0.83 | 17 | empty |
| 3 | 55 | 0.43 | 0.83 | 17 | empty |
| 4 | 125 | 0.41 | 0.75 | 27 | NAG, BMA, MAN |
| 5 | 62 | 0.31 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 105 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7PUK · Crystal structure of Endoglycosidase E GH18 domain from Enterococcus faecalis in complex… · 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 Q6U890
- Elsewhere: RCSB PDB 7PUK · PDBe 7PUK · UniProt Q6U890
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