7p9l

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase

Plesiomonas shigelloides 302-73

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	1,2-ETHANEDIOL × 22 DI(HYDROXYETHYL)ETHER × 7 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose × 2 ZINC ION × 4 POTASSIUM ION × 2 PHOSPHATE ION × 2 CHLORIDE ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 10–104； UniProt 2–96 Author chain BBB； PDBConstruct 10–104； UniProt 2–96

Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase

Plesiomonas shigelloides 302-73

UniProt R8APY9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	1,2-ETHANEDIOL × 22 DI(HYDROXYETHYL)ETHER × 7 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose × 2 ZINC ION × 4 POTASSIUM ION × 2 PHOSPHATE ION × 2 CHLORIDE ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R8APY9_PLESH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 116–417； UniProt 1–302 Author chain BBB； PDBConstruct 116–417； UniProt 1–302

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7p9l
Deposition date deposition_date	2021-07-27
Structure title title	N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate
Keywords keywords	N-acetylglucosamine recycling, carbohydrate kinase, ROK kinase., SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7p9l__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7p9l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7p9l__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.78 Å
Rg (electron density)	25.79 Å
Total Rg	26.49 Å
Atom count	4846
Residues	609
Excluded volume	86750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7p9l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
Molecular weight formula_weight	45960.1 kDa
EC 编号 ec_number	2.7.1.59
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,BBB
Atom count atom_count	5453

MAHHHHHHGSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQISSGLEVLFQGTMYYGFDIGGTKIEFGAFDADLVRVARERVATPTESYAAFLDAIVTLVNNADAEFGVKGTVGIGIPGIADVETGKLLTSNIPAAMGHTLQRDLEERLQRPVKIENDANCFALSEAWDEDLRGEPSVLGLILGTGVGGGLIFNGKVHSGRANIAGEIGHTRLPYDALKLLGMENAPIFPCGCKNSGCIDNYLSGRGFEQLYDHYFSEKLSAPEIIAHYEQGERRAVQHVERFMELLAICLANIFTCLDPHVVVLGGGLSNFELIYQELPKRLPAHLLHVAKLPKIIKARHGDAGGVRGAAFLNL

Source Source

Source organism organism	Plesiomonas shigelloides 302-73
NCBI taxonomy ID ncbi_taxonomy_id	1315976
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose
Molecular weight formula_weight	301.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	353

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Unit-cell length a length_a	114.508 Å
Unit-cell length b length_b	114.508 Å
Unit-cell length c length_c	119.266 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	76.252 Å
R factor r_factor	—
R_work r_work	0.1929
R_free r_free	0.2226

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7p9l__assembly_1__model_1

7p9l__assembly_1__model_1 | I(q)

7p9l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7p9l__assembly_1__model_1

7p9l__assembly_1__model_1 | I(q)

7p9l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)