SAXSdb — 2wya

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

HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	3-HYDROXY-3-METHYLGLUTARYL-COENZYME A × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	3-HYDROXY-3-METHYLGLUTARYL-COENZYME A × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMCS2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–460； UniProt 51–508 Author chain B； PDBConstruct 3–460； UniProt 51–508 Author chain C； PDBConstruct 3–460； UniProt 51–508 Author chain D； PDBConstruct 3–460； UniProt 51–508

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	2wya
Deposition date deposition_date	2009-11-13
Structure title title	CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 3-HYDROXY-3-METHYLGLUTARYL- COENZYME A SYNTHASE 2 (HMGCS2)
Keywords keywords	;STEROID BIOSYNTHESIS, CHOLESTEROL BIOSYNTHESIS, MITOCHONDRIA, MITOCHONDRION, PHOSPHOPROTEIN, MELAVONATE PATHWAY, STEROL BIOSYNTHESIS, THIOLASE, ACETYLATION, TRANSFERASE, LIPID SYNTHESIS, TRANSIT PEPTIDE, DISEASE MUTATION ;; TRANSFERASE
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.

2wya__assembly_1__model_1

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

Download this curve (.dat)

2wya__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wya__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.66 Å
Rg (electron density)	27.60 Å
Total Rg	28.32 Å
Atom count	7222
Residues	920
Excluded volume	127580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wya__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wya__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	HYDROXYMETHYLGLUTARYL-COA SYNTHASE, MITOCHONDRIAL
Molecular weight formula_weight	51316.0 kDa
EC 编号 ec_number	2.3.3.10
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	16074

SMPKDVGILALEVYFPAQYVDQTDLEKYNNVEAGKYTVGLGQTRMGFCSVQEDINSLCLTVVQRLMERIQLPWDSVGRLEVGTETIIDKSKAVKTVLMELFQDSGNTDIEGIDTTNACYGGTASLFNAANWMESSSWDGRYAMVVCGDIAVYPSGNARPTGGAGAVAMLIGPKAPLALERGLRGTHMENVYDFYKPNLASEYPIVDGKLSIQCYLRALDRCYTSYRKKIQNQWKQAGSDRPFTLDDLQYMIFHTPFCKMVQKSLARLMFNDFLSASSDTQTSLYKGLEAFGGLKLEDTYTNKDLDKALLKASQDMFDKKTKASLYLSTHNGNMYTSSLYGCLASLLSHHSAQELAGSRIGAFSYGSGLAASFFSFRVSQDAAPGSPLDKLVSSTSDLPKRLASRKCVSPEEFTEIMNQREQFYHKVNFSPPGDTNSLFPGTWYLERVDEQHRRKYARRPV

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	3-HYDROXY-3-METHYLGLUTARYL-COENZYME A
Molecular weight formula_weight	906.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1457

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2wyaA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	2wyaB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	2wyaC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

Domain ID domain_id	2wyaD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Thiolase/Chalcone synthase

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Unit-cell length a length_a	66.410 Å
Unit-cell length b length_b	83.514 Å
Unit-cell length c length_c	101.442 Å
Unit-cell angle α angle_alpha	100.00 °
Unit-cell angle β angle_beta	108.08 °
Unit-cell angle γ angle_gamma	96.30 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	31.358 Å
R factor r_factor	0.1616
R_work r_work	0.1614
R_free r_free	0.1840

CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 3-HYDROXY-3-METHYLGLUTARYL- COENZYME A SYNTHASE 2 (HMGCS2)

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

HYDROXYMETHYLGLUTARYL-COA SYNTHASE, 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

2wya__assembly_1__model_1

2wya__assembly_1__model_1 | I(q)

2wya__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 3-HYDROXY-3-METHYLGLUTARYL- COENZYME A SYNTHASE 2 (HMGCS2)

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

HYDROXYMETHYLGLUTARYL-COA SYNTHASE, 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

2wya__assembly_1__model_1

2wya__assembly_1__model_1 | I(q)

2wya__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)