SAXSdb — 9qz6

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

2-hydroxyacyl-CoA lyase

Actinomycetospora chiangmaiensis DSM 45062

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 MAGNESIUM ION × 6 ;~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (2~{S})-2-methyl-2,3-bis(oxidanyl)propanethioate ; × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HACL_ACTC0
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–601； UniProt 1–590 Author chain B； PDBConstruct 12–601； UniProt 1–590

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	9qz6
Deposition date deposition_date	2025-04-22
Last revision last_revision	2026-02-04
Structure title title	Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with 2-methylglyceryl-CoA and inactive cofactor 3-deaza-ThDP
Keywords keywords	ThDP, CoA, HACL, LYASE; LYASE
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.

9qz6__assembly_1__model_1

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

Download this curve (.dat)

9qz6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qz6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.08 Å
Rg (electron density)	36.99 Å
Total Rg	37.41 Å
Atom count	17566
Residues	2296
Excluded volume	307250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qz6__assembly_1__model_1`	tetrameric （4）	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	2-hydroxyacyl-CoA lyase
Molecular weight formula_weight	65362.2 kDa
EC 编号 ec_number	4.1.-.-
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	9873

MASHHHHHHSGMADRQDAERSGAGPARQSVPVASLVAEFLQEHGVDRVFGLQGGHIQPIWDQLARRGVRIVDVRDEGSAVHMAHAHTELTGQTAVAMVTAGPGVTNTVTAVANASVSRIPLLVIGGCPPIPQSNMGPLQDIPHTAILEPITRLARTLRSADQVLREFDEAWARASGDRGEPGPVYLEIPTDVLRRDVPPALQMREHLRAKPKRRPQPHPDDVAAVADLIRAAEKPAIISGRGARTTDGTDLVRLLDASGAAYLDTQESRGLVPDSHPAAVGSARSAVMRDTDLLITVGRQLDYQLGMGSPAVFPHAKVVRIADTASELIDNRRGEVEILAEPGAALAAIADALKDHTPDTSWRDELKAKHRKRAEDYRQALHSTENGADGHIHPNRIFGALDALDGDVLDLGETIMIADGGDLLSFGRLGITKARRYLDAGAFGCLGVATPFAIGAALAYPDRPVVAVTGDGAFGITATEIDTAVRHDAKIVVIVSNNRAWNIERYDQAENYGLVVGTDLADSDYAGVARAFGAHGERVTDPAELEGAIRRALANAPALVDVVTTQDAASPDSGKGLGFVPDYQALTPWNDAEVARRQEGIGSAWSHPQFEK

Source Source

Source organism organism	Actinomycetospora chiangmaiensis DSM 45062
NCBI taxonomy ID ncbi_taxonomy_id	1120948
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
Molecular weight formula_weight	423.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	;~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (2~{S})-2-methyl-2,3-bis(oxidanyl)propanethioate ;
Molecular weight formula_weight	869.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1065

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Unit-cell length a length_a	103.768 Å
Unit-cell length b length_b	146.493 Å
Unit-cell length c length_c	174.321 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.551 Å
Low-resolution limit resolution_low	84.680 Å
R factor r_factor	—
R_work r_work	0.1577
R_free r_free	0.1841

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with 2-methylglyceryl-CoA and inactive cofactor 3-deaza-ThDP

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

2-hydroxyacyl-CoA lyase

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

9qz6__assembly_1__model_1

9qz6__assembly_1__model_1 | I(q)

9qz6__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

7. Citations (1)

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with 2-methylglyceryl-CoA and inactive cofactor 3-deaza-ThDP

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

2-hydroxyacyl-CoA lyase

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

9qz6__assembly_1__model_1

9qz6__assembly_1__model_1 | I(q)

9qz6__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

7. Citations (1)