Research workbench
Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C56S C230S) in complex with N-acetyl-alpha-D-glucosamine (alpha-GlcNAc) and mannose 6-phosphate (M6P)
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
- 6PKI
- Type
- protein
- Length
- 1,193 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.293
- Source
- Danio rerio
- Molecule
- N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase
- UniProt
- F1QSF9
- Ligands
- NAG, M6P, NDG, CL
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.293 · 3 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase | protein | 301 | 19% helix, 36% strand | F1QSF9 |
| B, C | N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase | protein | 298 | 18% helix, 35% strand | F1QSF9 |
| D | N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase | protein | 296 | 18% helix, 36% strand | F1QSF9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- M6P · 6-O-phosphono-alpha-D-mannopyranose · sugar · 5 copies · chains A, B, C, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.76 | 0.81 | 62 | empty |
| 2 | 214 | 0.72 | 0.88 | 24 | empty |
| 3 | 729 | 0.72 | 0.78 | 80 | NDG |
| 4 | 204 | 0.71 | 0.88 | 26 | empty |
| 5 | 559 | 0.70 | 0.79 | 50 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1193 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1186 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 540 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 528 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6PKI · 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 6PKI · PDBe 6PKI · UniProt F1QSF9
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