3k6m

Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart.

Method: X-RAY DIFFRACTION

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

Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCOT1_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–481； UniProt 40–520 Author chain B； PDBConstruct 1–481； UniProt 40–520 Author chain C； PDBConstruct 1–481； UniProt 40–520 Author chain D； PDBConstruct 1–481； UniProt 40–520

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	3k6m
Deposition date deposition_date	2009-10-09
Structure title title	Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart.
Keywords keywords	SCOT, CoA Transferase, dynamic domain, glycerol, Mitochondrion, Transferase, Transit peptide; 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.

3k6m__assembly_1__model_1

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

Download this curve (.dat)

3k6m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3k6m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.77 Å
Rg (electron density)	29.22 Å
Total Rg	30.04 Å
Atom count	7059
Residues	926
Excluded volume	126730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3k6m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3k6m__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	Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
Molecular weight formula_weight	52294.0 kDa
EC 编号 ec_number	2.8.3.5
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,C,B
Atom count atom_count	16054

TKFYTDAVEAVKDIPNGATVLVGGFGLCGIPENLIGALLKTGVKELTAVSNNAGVDNFGLGLLLQSKQIKRMISSYVGENAEFERQYLAGELEVELTPQGTLAERIRAGGAGVPAFYTSTGYGTLVQEGGSPIKYNKDGSIAIASKPREVREFNGQHFILEEAIRGDFALVKAWKADQAGNVTFRKSARNFNLPMCKAAETTVVEVEEIVDIGSFAPEDIHIPKIYVHRLVKGEKYEKRIERLSVRKEEDVKTRSGKLGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGILGLGPYPLQNEVDADLINAGKETVTVLPGASYFSSDESFAMIRGGHVNLTMLGAMQVSKYGDLANWMIPGKLVKGMGGAMDLVSSAKTKVVVTMEHSAKGNAHKIMEKCTLPLTGKQCVNRIITEKAVFDVDRKKGLTLIELWEGLTVDDIKKSTGCDFAVSPKLIPMQQVTT

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

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	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	1581

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3k6ma1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.2 — CoA transferase alpha subunit-like

Domain ID domain_id	d3k6ma2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.3 — CoA transferase beta subunit-like

Domain ID domain_id	d3k6mb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.2 — CoA transferase alpha subunit-like

Domain ID domain_id	d3k6mb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.3 — CoA transferase beta subunit-like

Domain ID domain_id	d3k6mc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.2 — CoA transferase alpha subunit-like

Domain ID domain_id	d3k6mc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.3 — CoA transferase beta subunit-like

Domain ID domain_id	d3k6md1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.2 — CoA transferase alpha subunit-like

Domain ID domain_id	d3k6md2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.3 — CoA transferase beta subunit-like

CATH v4.4 (8 domains)

Domain ID domain_id	3k6mA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	3k6mA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	3k6mB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	3k6mB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	3k6mC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	3k6mC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	3k6mD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	3k6mD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

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Unit-cell length a length_a	73.715 Å
Unit-cell length b length_b	133.566 Å
Unit-cell length c length_c	102.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1657
R_work r_work	0.1650
R_free r_free	0.1854

Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart.

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

Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, 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

3k6m__assembly_1__model_1

3k6m__assembly_1__model_1 | I(q)

3k6m__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart.

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

Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, 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

3k6m__assembly_1__model_1

3k6m__assembly_1__model_1 | I(q)

3k6m__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)