MolNFT v1 · #165617 · protein
Xenopus laevis N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) (C46S C219S C453S C480S C486S) with ctd mostly flexible
6U11 · EGF-like domain-containing protein: “Xenopus laevis N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) (C46S C219S C453S…”. X-ray diffraction, 3 ligands (NAG, FUC, K), 3 pockets (best druggability 0.70).…
- PDB
- 6U11
- Type
- protein
- Length
- 316 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EGF-like domain-containing protein
- UniProt
- A0A1L8HDP6
- Ligands
- NAG, FUC, K
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EGF-like domain-containing protein | protein | 316 | 17% helix, 33% strand | A0A1L8HDP6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- FUC · alpha-L-fucopyranose · sugar
- K · Potassium ion · metal · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.70 | 0.98 | 19 | K |
| 2 | 79 | 0.40 | 0.79 | 20 | empty |
| 3 | 57 | 0.32 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6U11 · Xenopus laevis N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA)… · 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 A0A1L8HDP6
- Elsewhere: RCSB PDB 6U11 · PDBe 6U11 · UniProt A0A1L8HDP6
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