SAXSdb — 2wd9

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

ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IBUPROFEN × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	IBUPROFEN × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	IBUPROFEN × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACS2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–569； UniProt 32–576 Author chain B； PDBConstruct 25–569； UniProt 32–576 Author chain C； PDBConstruct 25–569； UniProt 32–576

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	2wd9
Deposition date deposition_date	2009-03-21
Structure title title	CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A (L64P MUTATION) IN COMPLEX WITH IBUPROFEN
Keywords keywords	;NUCLEOTIDE-BINDING, FATTY ACID METABOLISM, TRANSIT PEPTIDE, LIPID METABOLISM, NUCLEOTIDE BINDING, MITOCHONDRION, METAL-BINDING, LIGASE ACTIVITY, MEDIUM-CHAIN FATTY ACID, FATTY ACID METABOLIC PROCESS, LIGASE, MAGNESIUM, ATP-BINDING ;; LIGASE
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.

2wd9__assembly_1__model_1

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

Download this curve (.dat)

2wd9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wd9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.15 Å
Rg (electron density)	22.97 Å
Total Rg	23.88 Å
Atom count	4124
Residues	533
Excluded volume	73959 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wd9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wd9__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2wd9__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
Molecular weight formula_weight	63206.4 kDa
EC 编号 ec_number	6.2.1.2
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	12720

MGHHHHHHSSGVDLGTENLYFQSMSLQWGHQEVPAKFNFASDVLDHWADMEKAGKRPPSPALWWVNGKGKELMWNFRELSENSQQAANVLSGACGLQRGDRVAVVLPRVPEWWLVILGCIRAGLIFMPGTIQMKSTDILYRLQMSKAKAIVAGDEVIQEVDTVASECPSLRIKLLVSEKSCDGWLNFKKLLNEASTTHHCVETGSQEASAIYFTSGTSGLPKMAEHSYSSLGLKAKMDAGWTGLQASDIMWTISDTGWILNILCSLMEPWALGACTFVHLLPKFDPLVILKTLSSYPIKSMMGAPIVYRMLLQQDLSSYKFPHLQNCVTVGESLLPETLENWRAQTGLDIRESYGQTETGLTCMVSKTMKIKPGYMGTAASCYDVQIIDDKGNVLPPGTEGDIGIRVKPIRPIGIFSGYVDNPDKTAANIRGDFWLLGDRGIKDEDGYFQFMGRADDIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEWKMSGKARA

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	TRICHOPLUSIA NI

Entity 2 Entity 2 non-polymer

Description description	IBUPROFEN
Molecular weight formula_weight	206.3 kDa
Source method src_method	syn
Copy count entity_count	3

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	215

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2wd9a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamily	e.23.1 — Acetyl-CoA synthetase-like
Family Family family	e.23.1.0 — automated matches

Domain ID domain_id	d2wd9b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamily	e.23.1 — Acetyl-CoA synthetase-like
Family Family family	e.23.1.0 — automated matches

Domain ID domain_id	d2wd9c_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamily	e.23.1 — Acetyl-CoA synthetase-like
Family Family family	e.23.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2wd9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	2wd9A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

Domain ID domain_id	2wd9B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	2wd9B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

Domain ID domain_id	2wd9C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	2wd9C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

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Unit-cell length a length_a	98.320 Å
Unit-cell length b length_b	98.320 Å
Unit-cell length c length_c	381.440 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	24

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	38.920 Å
R factor r_factor	0.2360
R_work r_work	0.2350
R_free r_free	0.2550

CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A (L64P MUTATION) IN COMPLEX WITH IBUPROFEN

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

ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL

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

2wd9__assembly_1__model_1

2wd9__assembly_1__model_1 | I(q)

2wd9__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A (L64P MUTATION) IN COMPLEX WITH IBUPROFEN

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

ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL

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

2wd9__assembly_1__model_1

2wd9__assembly_1__model_1 | I(q)

2wd9__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)