7P7W: PDB entry 7P7W

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and ADP. Determined by X-ray diffraction at 1.57 Å resolution. Released 3 Aug 2022.

Method: X-ray diffraction
Resolution: 1.57 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Plesiomonas shigelloides 302-73
Chains: 2
Atoms: 5,811
Mol. weight: 95.33 kDa
Ligands: IPA, ZN, NDG, ADP
Released: 3 Aug 2022

Explore 7P7W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P7W contains 37 α-helices and 36 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: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	11-17	7	1
β-strand	23-30	8	1
α-helix	36-54	19
β-strand	59-64	6	1
β-strand	67-68	2	2
β-strand	74	1	3
β-strand	75-76	2	2
α-helix	81-83	3
β-strand	87	1	3
α-helix	88-96	9
β-strand	100-104	5	1
α-helix	105-115	11
β-strand	124-130	7	4
β-strand	134-140	7	4
β-strand	143-145	3	4
α-helix	155-157	3
β-strand	159	1	5
α-helix	160	1
β-strand	161	1	6
α-helix	162-167	6
α-helix	170-172	3
β-strand	177	1	7
β-strand	183	1	7
β-strand	185	1	5
α-helix	186-188	3
α-helix	192-203	12
α-helix	209-217	9
α-helix	221-245	25
β-strand	249-253	5	4
α-helix	255-258	4
α-helix	261-269	9
α-helix	271-273	3
α-helix	280-281	2
β-strand	282-285	4	4
α-helix	292-298	7
α-helix	299-301	3

Chain BBB: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	8
β-strand	11-17	7	8
β-strand	23-30	8	8
α-helix	31-32	2
α-helix	36-54	19
β-strand	59-64	6	8
β-strand	67-68	2	9
β-strand	75-76	2	9
α-helix	81-83	3
α-helix	88-96	9
β-strand	100-104	5	8
α-helix	105-115	11
β-strand	124-130	7	10
β-strand	134-140	7	10
β-strand	143-145	3	10
α-helix	155-157	3
β-strand	159	1	11
α-helix	160	1
β-strand	161	1	6
α-helix	162-167	6
α-helix	170-172	3
β-strand	177	1	12
β-strand	183	1	12
β-strand	185	1	11
α-helix	186-188	3
α-helix	192-203	12
α-helix	209-217	9
α-helix	221-245	25
β-strand	249-253	5	10
α-helix	255-258	4
α-helix	261-269	9
α-helix	271-273	3
α-helix	280-281	2
β-strand	282-285	4	10
α-helix	292-298	7
α-helix	299-301	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase	AAA, BBB	protein	417	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Plesiomonas shigelloides 302-73	Q12306 (AlphaFold model), R8APY9 (AlphaFold model)

Sequence of entity 1 (AAA, BBB), FASTA

>7P7W_1 Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase (chains AAA, BBB)
MAHHHHHHGSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAF
AKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQISSGLEVLFQGTMYYGF
DIGGTKIEFGAFDADLVRVARERVATPTESYAAFLDAIVTLVNNADAEFGVKGTVGIGIP
GIADVETGKLLTSNIPAAMGHTLQRDLEERLQRPVKIENDANCFALSEAWDEDLRGEPSV
LGLILGTGVGGGLIFNGKVHSGRANIAGEIGHTRLPYDALKLLGMENAPIFPCGCKNSGC
IDNYLSGRGFEQLYDHYFSEKLSAPEIIAHYEQGERRAVQHVERFMELLAICLANIFTCL
DPHVVVLGGGLSNFELIYQELPKRLPAHLLHVAKLPKIIKARHGDAGGVRGAAFLNL

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	1
ZN	Zinc ion	Zn	4
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	C8 H15 N O6	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Water and common crystallization additives (IMD, PEG, K, EDO, GOL) 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:

3UF8 1.5 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with a G95A…
6UKZ 1.52 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 6
3UQA 1.55 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface…
3VAW 1.55 Å, Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface…
5YCA 1.57 Å, Crystal structure of inner membrane protein Bqt4 in complex with LEM2
1EUV 1.6 Å, X-ray structure of the C-terminal ULP1 protease domain in complex with SMT3, the yeast…
6UKU 1.68 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 3
7P7I 1.7 Å, Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides
6UKM 1.74 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound MSA-2
4G50 1.75 Å, Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface…
7P9L 1.75 Å, N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with…
6UL0 1.76 Å, STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 4

Browse structure collections

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