Research workbench
Guinea pig N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) catalytic domain (C51S C221S) in complex with N-acetyl-alpha-D-glucosamine (alpha-glcnac) and mannose 6-phosphate (M6P)
Analyse Guinea pig 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
- 6PKU
- Type
- protein
- Length
- 1,053 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa)
- UniProt
- H0VTT5
- Ligands
- M6P, NDG, NAG
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) | protein | 263 | 17% helix, 37% strand | H0VTT5 |
| B | N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) | protein | 264 | 16% helix, 37% strand | H0VTT5 |
Ligands and binding sites
- M6P · 6-O-phosphono-alpha-D-mannopyranose · ligand · 4 copies · chains A, B, C, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.67 | 0.85 | 26 | empty |
| 2 | 217 | 0.67 | 0.85 | 27 | empty |
| 3 | 138 | 0.55 | 0.82 | 26 | NDG |
| 4 | 132 | 0.55 | 0.82 | 25 | NDG |
| 5 | 115 | 0.53 | 0.82 | 25 | NDG |
Interfaces
3 interfaces between chains.
- B–D · 1124 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1120 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 711 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6PKU · Guinea pig 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 H0VTT5
- Elsewhere: RCSB PDB 6PKU · PDBe 6PKU · UniProt H0VTT5
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