MolNFT v1 · #160439 · 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, 4 ligands (M6P, NAG, NDG). MolNFT v1 #160439 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6PKI
Type: protein
Length: 1,193 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: F1QSF9
Ligands: M6P, NAG, NDG, CL

Structure

x-ray diffraction · 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

M6P · 6-O-phosphono-alpha-D-mannopyranose · ligand · 5 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 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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