MolNFT v1 · #160455 · protein
Guinea pig N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) catalytic domain auto-inhibited by pro- peptide
6PKY: “Guinea pig N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) catalytic domain…”. X-ray diffraction, 4 ligands (NAG, FUC, CL), 18 pockets (best druggability 0.71). MolNFT v1 #160455 on GenesisL1: 3D…
- PDB
- 6PKY
- Type
- protein
- Length
- 1,139 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
- NAG, FUC, CL, BR
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) | protein | 286 | 15% helix, 36% strand | H0VTT5 |
| B | N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) | protein | 285 | 15% helix, 33% strand | H0VTT5 |
| C | N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) | protein | 285 | 14% helix, 36% strand | H0VTT5 |
| D | N-acetylglucosamine-1-phosphodiester alpha-N- acetylglucosaminidase (nagpa) | protein | 283 | 14% helix, 36% strand | H0VTT5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar
- CL · Chloride ion · ion · 32 copies · chains A, B, C, D
- BR · Bromide ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.71 | 0.87 | 33 | BR, CL |
| 2 | 245 | 0.71 | 0.86 | 31 | CL |
| 3 | 244 | 0.68 | 0.85 | 40 | BR |
| 4 | 154 | 0.68 | 0.88 | 28 | BR |
| 5 | 166 | 0.65 | 0.86 | 30 | BR, CL |
Interfaces
3 interfaces between chains.
- C–D · 1200 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1189 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 990 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6PKY · 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 6PKY · PDBe 6PKY · UniProt H0VTT5
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