SAXSdb — 6ih0

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

UDP-3-O-acyl-N-acetylglucosamine deacetylase

Aquifex aeolicus (strain VF5)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;N-[(2S)-3-azanyl-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]-4-[4-[(1R,2R)-2-(hydroxymethyl)cyclopropyl]buta -1,3-diynyl]benzamide ; × 1 ZINC ION × 1 methyl (2S)-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LPXC_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–271； UniProt 1–271

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	6ih0
Deposition date deposition_date	2018-09-27
Structure title title	Aquifex aeolicus LpxC complex with ACHN-975
Keywords keywords	Inhibitor, Complex, ANTIBIOTIC, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

6ih0__assembly_1__model_1

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

Download this curve (.dat)

6ih0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ih0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.81 Å
Rg (electron density)	17.74 Å
Total Rg	18.78 Å
Atom count	2202
Residues	267
Excluded volume	39566 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ih0__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	UDP-3-O-acyl-N-acetylglucosamine deacetylase
Molecular weight formula_weight	32060.7 kDa
EC 编号 ec_number	3.5.1.108
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2552

MGLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQKLTRLEHHHHHH

Source Source

Source organism organism	Aquifex aeolicus (strain VF5)
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	;N-[(2S)-3-azanyl-3-methyl-1-(oxidanylamino)-1-oxidanylidene-butan-2-yl]-4-[4-[(1R,2R)-2-(hydroxymethyl)cyclopropyl]buta -1,3-diynyl]benzamide ;
Molecular weight formula_weight	369.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	methyl (2S)-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate
Molecular weight formula_weight	246.3 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	350

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6ih0a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.7 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC

Domain ID domain_id	d6ih0a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.7 — UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC

CATH v4.4 (2 domains)

Domain ID domain_id	6ih0A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	20 — lpxc deacetylase, domain 1

Domain ID domain_id	6ih0A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1700 — lpxc deacetylase, domain 1
Homologous superfamily homologous superfamily	10 — lpxc deacetylase, domain 2

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Unit-cell length a length_a	65.569 Å
Unit-cell length b length_b	65.569 Å
Unit-cell length c length_c	131.595 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	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	1.210 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1645
R_work r_work	0.1641
R_free r_free	0.1824

Aquifex aeolicus LpxC complex with ACHN-975

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

UDP-3-O-acyl-N-acetylglucosamine deacetylase

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

6ih0__assembly_1__model_1

6ih0__assembly_1__model_1 | I(q)

6ih0__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Aquifex aeolicus LpxC complex with ACHN-975

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

UDP-3-O-acyl-N-acetylglucosamine deacetylase

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

6ih0__assembly_1__model_1

6ih0__assembly_1__model_1 | I(q)

6ih0__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)