7P9P: PDB entry 7P9P

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and AMP-PNP inhibitor. Determined by X-ray diffraction at 2.11 Å resolution. Released 10 Aug 2022.

Method
X-ray diffraction
Resolution
2.11 Å
Organisms
Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Plesiomonas shigelloides 302-73
Chains
2
Atoms
5,228
Mol. weight
95.26 kDa
Ligands
NDG, ANP, ZN
Released
10 Aug 2022

Explore 7P9P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P9P contains 33 α-helices and 34 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain AAA: 16 helices, 17 β-strands

ElementResiduesLengthSheet
β-strand1-771
β-strand11-1881
β-strand23-3081
α-helix36-5419
β-strand59-6461
β-strand67-6822
β-strand75-7622
α-helix88-958
β-strand100-10451
α-helix105-11511
β-strand124-13073
β-strand134-14073
β-strand143-14423
α-helix155-1573
β-strand15914
α-helix1601
β-strand16115
α-helix162-1676
α-helix170-1723
β-strand17716
β-strand18316
β-strand18514
α-helix186-1883
α-helix192-20312
α-helix209-2179
α-helix221-24525
β-strand249-25353
α-helix255-2584
α-helix261-2699
α-helix271-2733
β-strand282-28543
α-helix292-2987
α-helix299-3013
Chain BBB: 17 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand1-777
β-strand11-1887
β-strand23-3087
α-helix36-5419
β-strand59-6467
β-strand67-6828
β-strand75-7628
α-helix81-833
α-helix88-958
β-strand100-10457
α-helix105-11511
β-strand124-13079
β-strand134-14079
β-strand143-14429
α-helix155-1573
β-strand159110
α-helix1601
β-strand16115
α-helix162-1676
α-helix170-1723
β-strand177111
β-strand183111
β-strand185110
α-helix186-1883
α-helix192-20312
α-helix209-2179
α-helix221-24525
β-strand249-25359
α-helix255-2584
α-helix261-2699
α-helix271-2733
β-strand282-28549
α-helix292-2987
α-helix299-3013

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinaseAAA, BBBprotein417Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Plesiomonas shigelloides 302-73Q12306 (AlphaFold model), R8APY9 (AlphaFold model)
Sequence of entity 1 (AAA, BBB), FASTA
>7P9P_1 Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase (chains AAA, BBB)
MAHHHHHHGSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAF
AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQISSGLEVLFQGTMYYGF
DIGGTKIEFGAFDADLVRVARERVATPTESYAAFLDAIVTLVNNADAEFGVKGTVGIGIP
GIADVETGKLLTSNIPAAMGHTLQRDLEERLQRPVKIENDANCFALSEAWDEDLRGEPSV
LGLILGTGVGGGLIFNGKVHSGRANIAGEIGHTRLPYDALKLLGMENAPIFPCGCKNSGC
IDNYLSGRGFEQLYDHYFSEKLSAPEIIAHYEQGERRAVQHVERFMELLAICLANIFTCL
DPHVVVLGGGLSNFELIYQELPKRLPAHLLHVAKLPKIIKARHGDAGGVRGAAFLNL

Ligands and cofactors

IDNameFormulaCopies
NDG2-acetamido-2-deoxy-alpha-D-glucopyranoseC8 H15 N O62
ANPPhosphoaminophosphonic acid-adenylate esterC10 H17 N6 O12 P32
ZNZinc ionZn4

Water and common crystallization additives (K, EDO, PGE, PEG) are not listed.

Primary citation

Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases. Cross, A.R., Roy, S., Vivoli Vega, M. et al. J Biol Chem (2022). DOI 10.1016/j.jbc.2022.101903

Other PDB entries of the same protein (UniProt Q12306 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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