Research workbench
Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) catalytic domain auto-inhibited by pro- peptide
Analyse Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PKG
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase
- UniProt
- F1QSF9
- Ligands
- I2I, NAG, MAN, BMA, FUC, IOD
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase | protein | 307 | 19% helix, 34% strand | F1QSF9 |
Ligands and binding sites
- I2I · molecular iodine · ligand · 15 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- IOD · Iodide ion · ion · 48 copies · chains A, B
- P6G · Hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.71 | 0.87 | 24 | I2I |
| 2 | 75 | 0.48 | 0.83 | 19 | empty |
| 3 | 186 | 0.48 | 0.75 | 25 | I2I |
| 4 | 69 | 0.47 | 0.83 | 19 | empty |
| 5 | 173 | 0.45 | 0.75 | 26 | IOD, I2I |
Interfaces
1 interface between chains.
- A–B · 1184 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6PKG · Zebrafish 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 F1QSF9
- Elsewhere: RCSB PDB 6PKG · PDBe 6PKG · UniProt F1QSF9
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