SAXSdb — 7jmk

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

Succinate--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） GUANOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial × 1 （P53590） 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 Author chain C； 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	Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial × 1 （O19069） GUANOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial × 1 （O19069） 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, 3
Chains and sequence ranges	Author chain B； PDBConstruct 2–395； UniProt 40–433 Author chain D； 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	7jmk
Deposition date deposition_date	2020-08-01
Structure title title	GTP-specific succinyl-CoA synthetase complexed with Mg-GDP in space group P32
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.

7jmk__assembly_1__model_1

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

Download this curve (.dat)

7jmk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7jmk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.95 Å
Rg (electron density)	27.05 Å
Total Rg	27.80 Å
Atom count	10269
Residues	676
Excluded volume	91239 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7jmk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7jmk__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 (6)

Entity 1 Entity 1 polymer

Description description	Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
Molecular weight formula_weight	32089.9 kDa
EC 编号 ec_number	6.2.1.4,6.2.1.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	20236

SYTASRKHLYVDKNTKVICQGFTGKQGTFHSQQALEYGTNLVGGTTPGKGGKTHLGLPVFNTVKEAKEQTGATASVIYVPPPFAAAAINEAIDAEVPLVVCITEGIPQQDMVRVKHRLLRQGKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFTDCLEIFLNDPATEGIILIGEIGGNAEENAAEFLKQHNSGPKSKPVVSFIAGLTAPPGRRMGHAGAIIAGGKGGAKEKITALQSAGVVVSMSPAQLGTTIYKEFEKRKML

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 polymer

Description description	Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial
Molecular weight formula_weight	42711.9 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	D

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 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d7jmka1
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	d7jmka2
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	d7jmkb1
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	d7jmkb2
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	d7jmkc1
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	d7jmkc2
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	d7jmkd1
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	d7jmkd2
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	7jmkB01
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	99.762 Å
Unit-cell length b length_b	99.762 Å
Unit-cell length c length_c	134.206 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	53.000 Å
R factor r_factor	0.2415
R_work r_work	0.2399
R_free r_free	0.2694

GTP-specific succinyl-CoA synthetase complexed with Mg-GDP in space group P32

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

Succinate--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

7jmk__assembly_1__model_1

7jmk__assembly_1__model_1 | I(q)

7jmk__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (8 domains)

CATH v4.4 (1 domains)

7. Citations (1)

GTP-specific succinyl-CoA synthetase complexed with Mg-GDP in space group P32

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

Succinate--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

7jmk__assembly_1__model_1

7jmk__assembly_1__model_1 | I(q)

7jmk__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (8 domains)

CATH v4.4 (1 domains)

7. Citations (1)