MolNFT v2 · #161596 · protein
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)
6PKI: “Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C56S…”. X-ray diffraction at 2.293, 4 ligands (NAG, M6P, NDG). MolNFT v2 #161596 on GenesisL1: 3D structure, binding sites and…
- 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
- UniProt
- F1QSF9
- Ligands
- NAG, M6P, NDG, CL
Structure
x-ray diffraction · resolution 2.293 · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 301 | — | F1QSF9 |
| B, C | — | protein | 298 | — | F1QSF9 |
| D | — | protein | 296 | — | 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
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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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