1yhc

Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with cacodylate

Method: X-RAY DIFFRACTION

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

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 5 CACODYLATE ION × 2 SULFATE ION × 2 CHLORIDE ION × 3 PALMITOLEIC ACID × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 5 CACODYLATE ION × 2 SULFATE ION × 2 CHLORIDE ION × 3 PALMITOLEIC ACID × 2 GLYCEROL × 1 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 3 CACODYLATE ION × 1 SULFATE ION × 1 CHLORIDE ION × 2 PALMITOLEIC ACID × 1 GLYCEROL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2 CACODYLATE ION × 1 SULFATE ION × 1 CHLORIDE ION × 1 PALMITOLEIC ACID × 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 1–270； UniProt 2–271 Author chain B； PDBConstruct 1–270； UniProt 2–271

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	1yhc
Deposition date deposition_date	2005-01-07
Structure title title	Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with cacodylate
Keywords keywords	x-ray crystallography; A.aeolicus, HYDROLASE; HYDROLASE
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.

1yhc__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yhc__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yhc__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	18.70 Å
Rg (electron density)	17.68 Å
Total Rg	18.69 Å
Atom count	2187
Residues	266
Excluded volume	39387 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yhc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yhc__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yhc__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1yhc__assembly_4__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 (8)

Entity 1 Entity 1 polymer

Description description	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
Molecular weight formula_weight	30858.3 kDa
EC 编号 ec_number	3.5.1.-
Mutation mutation	C181A, C-terminal deletion of D284-L294
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4721

GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQKLTR

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	PALMITOLEIC ACID
Molecular weight formula_weight	254.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	319

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yhca1
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	d1yhca2
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	d1yhcb1
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	d1yhcb2
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 (4 domains)

Domain ID domain_id	1yhcA01
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	1yhcA02
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

Domain ID domain_id	1yhcB01
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	1yhcB02
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	101.279 Å
Unit-cell length b length_b	101.279 Å
Unit-cell length c length_c	122.745 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 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1823
R_work r_work	0.1800
R_free r_free	0.2100

Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with cacodylate

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

UDP-3-O-[3-hydroxymyristoyl] 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

1yhc__assembly_3__model_1

1yhc__assembly_3__model_1 | I(q)

1yhc__assembly_3__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Aquifex aeolicus LpxC deacetylase complexed with cacodylate

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

UDP-3-O-[3-hydroxymyristoyl] 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

1yhc__assembly_3__model_1

1yhc__assembly_3__model_1 | I(q)

1yhc__assembly_3__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)