› 7p7w

X-ray diffraction
1.57Å resolution

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and ADP

Released:
DOI: 10.2210/pdb7p7w/pdb
PDB entry 7p7w coloured by chain, front view.
PDB entry 7p7w coloured by chain, side view.
PDB entry 7p7w coloured by chain, top view.
Source organisms:
Primary publication:
Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases
Cross AR, Roy S, Vivoli Vega M, Rejzek M, Nepogodiev SA, Cliff M, Salmon D, Isupov MN, Field RA, Prior JL, Harmer NJ
J. Biol. Chem. (2022)

Function and Biology Details

Reaction catalysed: 
ATP + N-acetyl-D-glucosamine = ADP + N-acetyl-D-glucosamine 6-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171339 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-acetyl-D-glucosamine kinase; Ubiquitin-like protein SMT3 Chains: AAA, BBB
Molecule details ›
Chains: AAA, BBB
Length: 417 amino acids
Theoretical weight: 45.96 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12306 (Residues: 2-96; Coverage: 94%)
  • Canonical: R8APY9 (Residues: 1-302; Coverage: 100%)
Gene names: D9719.15, PLESHI_11010, SMT3, YDR510W, nagK
Sequence domains:

Ligands and Environments

9 bound ligands:
Ligand ADP 2 x ADP
Ligand GOL 3 x GOL
Ligand IMD 4 x IMD
Ligand NDG 2 x NDG
Ligand ZN 4 x ZN
Ligand EDO 17 x EDO
Ligand PEG 1 x PEG
Ligand K 2 x K
Ligand IPA 1 x IPA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P3221
Unit cell:
a: 115.1Å b: 115.1Å c: 120.304Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.186 0.211
Expression system: Escherichia coli BL21(DE3)

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