6xru

GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme A, magnesium ions and succinates

Method: X-RAY DIFFRACTION

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

Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial

Sus scrofa

UniProt O19069

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial × 1 （P53590） DESULFO-COENZYME A × 1 SUCCINIC ACID × 2 GLYCEROL × 4 1,2-ETHANEDIOL × 2 PHOSPHATE ION × 1 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUCA_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–305； UniProt 42–346

Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial

Sus scrofa

UniProt P53590

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial × 1 （O19069） DESULFO-COENZYME A × 1 SUCCINIC ACID × 2 GLYCEROL × 4 1,2-ETHANEDIOL × 2 PHOSPHATE ION × 1 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUCB2_PIG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–395； UniProt 40–433

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	6xru
Deposition date deposition_date	2020-07-13
Structure title title	GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme A, magnesium ions and succinates
Keywords keywords	Complex, LIGASE; 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.

6xru__assembly_1__model_1

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

Download this curve (.dat)

6xru__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6xru__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.06 Å
Rg (electron density)	27.38 Å
Total Rg	28.04 Å
Atom count	10803
Residues	702
Excluded volume	95788 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6xru__assembly_1__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 (9)

Entity 1 Entity 1 polymer

Description description	Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
Molecular weight formula_weight	33131.0 kDa
EC 编号 ec_number	6.2.1.4,6.2.1.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11838

SYTASRKHLYVDKNTKVICQGFTGKQGTFHSQQALEYGTNLVGGTTPGKGGKTHLGLPVFNTVKEAKEQTGATASVIYVPPPFAAAAINEAIDAEVPLVVCITEGIPQQDMVRVKHRLLRQGKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFTDCLEIFLNDPATEGIILIGEIGGNAEENAAEFLKQHNSGPKSKPVVSFIAGLTAPPGRRMGHAGAIIAGGKGGAKEKITALQSAGVVVSMSPAQLGTTIYKEFEKRKMLLVHHHHHH

Source Source

Source organism organism	Sus scrofa
Common name common_name	Pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
Molecular weight formula_weight	42635.7 kDa
EC 编号 ec_number	6.2.1.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQILAGGRGKGVFSSGLKGGVHLTKDPEVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRSCNGPVLVGSPQGGVDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFLGPLQNQAADQIKKLYNLFLKIDATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDKSENEPIENEAAKYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKESQVYQAFKLLTADPKVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVVRLEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVTKK

Source Source

Source organism organism	Sus scrofa
Common name common_name	Pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	DESULFO-COENZYME A
Molecular weight formula_weight	735.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	738

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6xrua1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.8 — CoA-binding domain

Domain ID domain_id	d6xrua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.4 — Succinyl-CoA synthetase domains
Family Family family	c.23.4.1 — Succinyl-CoA synthetase domains

Domain ID domain_id	d6xrua3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6xrub1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.4 — Succinyl-CoA synthetase, beta-chain, N-terminal domain

Domain ID domain_id	d6xrub2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.4 — Succinyl-CoA synthetase domains
Family Family family	c.23.4.1 — Succinyl-CoA synthetase domains

CATH v4.4 (1 domains)

Domain ID domain_id	6xruB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

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Unit-cell length a length_a	86.041 Å
Unit-cell length b length_b	81.246 Å
Unit-cell length c length_c	50.386 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	48.760 Å
R factor r_factor	0.1698
R_work r_work	0.1686
R_free r_free	0.1842

GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme A, magnesium ions and succinates

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

Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Succinate--CoA ligase [GDP-forming] subunit beta, 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

6xru__assembly_1__model_1

6xru__assembly_1__model_1 | I(q)

6xru__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (5 domains)

CATH v4.4 (1 domains)

7. Citations (1)

GTP-specific succinyl-CoA synthetase complexed with desulfo-coenzyme A, magnesium ions and succinates

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

Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, 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

Succinate--CoA ligase [GDP-forming] subunit beta, 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

6xru__assembly_1__model_1

6xru__assembly_1__model_1 | I(q)

6xru__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (5 domains)

CATH v4.4 (1 domains)

7. Citations (1)