SAXSdb — 6c12

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

Succinate dehydrogenase flavoprotein subunit

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	FAD assembly factor SdhE × 1 （P64559） FLAVIN-ADENINE DINUCLEOTIDE × 1 SODIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	FAD assembly factor SdhE × 1 （P64559） FLAVIN-ADENINE DINUCLEOTIDE × 1 SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDHA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–588； UniProt 1–588 Author chain B； PDBConstruct 1–588； UniProt 1–588

FAD assembly factor SdhE

Escherichia coli (strain K12)

UniProt P64559

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Succinate dehydrogenase flavoprotein subunit × 1 （P0AC41） FLAVIN-ADENINE DINUCLEOTIDE × 1 SODIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Succinate dehydrogenase flavoprotein subunit × 1 （P0AC41） FLAVIN-ADENINE DINUCLEOTIDE × 1 SODIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDHE_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 15–101； UniProt 2–88 Author chain D； PDBConstruct 15–101； UniProt 2–88

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	6c12
Deposition date deposition_date	2018-01-03
Structure title title	SDHA-SDHE complex
Keywords keywords	Succinate dehydrogenase, Assembly factor, Oxidoreductase-Chaperon complex; Oxidoreductase/Chaperon
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.

6c12__assembly_1__model_1

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

Download this curve (.dat)

6c12__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6c12__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.88 Å
Rg (electron density)	23.82 Å
Total Rg	24.66 Å
Atom count	4891
Residues	623
Excluded volume	85996 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6c12__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6c12__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 (5)

Entity 1 Entity 1 polymer

Description description	Succinate dehydrogenase flavoprotein subunit
Molecular weight formula_weight	64502.8 kDa
EC 编号 ec_number	1.3.5.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	10122

MKLPVREFDAVVIGAGGAGMRAALQISQSGQTCALLSKVFPTRSHTVSAQGGITVALGNTHEDNWEWHMYDTVKGSDYIGDQDAIEYMCKTGPEAILELEHMGLPFSRLDDGRIYQRPFGGQSKNFGGEQAARTAAAADRTGHALLHTLYQQNLKNHTTIFSEWYALDLVKNQDGAVVGCTALCIETGEVVYFKARATVLATGGAGRIYQSTTNAHINTGDGVGMAIRAGVPVQDMEMWQFHPTGIAGAGVLVTEGCRGEGGYLLNKHGERFMERYAPNAKDLAGRDVVARSIMIEIREGRGCDGPWGPHAKLKLDHLGKEVLESRLPGILELSRTFAHVDPVKEPIPVIPTCHYMMGGIPTKVTGQALTVNEKGEDVVVPGLFAVGEIACVSVHGANRLGGNSLLDLVVFGRAAGLHLQESIAEQGALRDASESDVEASLDRLNRWNNNRNGEDPVAIRKALQECMQHNFSVFREGDAMAKGLEQLKVIRERLKNARLDDTSSEFNTQRVECLELDNLMETAYATAVSANFRTESRGAHSRFDFPDRDDENWLCHSLYLPESESMTRRSVNMEPKLRPAFPPKIRTY

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	FAD assembly factor SdhE
Molecular weight formula_weight	12050.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C

MGSSHHHHHHSQDPDINNKARIHWACRRGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELEMMVRLIQTRNRERGPVAI

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	357

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6c12a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

Domain ID domain_id	d6c12a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	d6c12a3
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.3 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
Family Family family	a.7.3.1 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain

Domain ID domain_id	d6c12b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

Domain ID domain_id	d6c12b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	d6c12b3
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.3 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
Family Family family	a.7.3.1 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain

Domain ID domain_id	d6c12c_
Class class	a — All alpha proteins
Fold Fold fold	a.218 — YgfY-like
Superfamily Superfamily superfamily	a.218.1 — YgfY-like
Family Family family	a.218.1.0 — automated matches

Domain ID domain_id	d6c12d_
Class class	a — All alpha proteins
Fold Fold fold	a.218 — YgfY-like
Superfamily Superfamily superfamily	a.218.1 — YgfY-like
Family Family family	a.218.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6c12C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	250 — Flavinator of succinate dehydrogenase

Domain ID domain_id	6c12D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	250 — Flavinator of succinate dehydrogenase

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Unit-cell length a length_a	52.980 Å
Unit-cell length b length_b	100.030 Å
Unit-cell length c length_c	232.130 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	48.890 Å
R factor r_factor	0.2019
R_work r_work	0.1989
R_free r_free	0.2582

SDHA-SDHE complex

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

Succinate dehydrogenase flavoprotein subunit

State in the Current Structure

Other States of the Same Protein in the Database

FAD assembly factor SdhE

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

6c12__assembly_1__model_1

6c12__assembly_1__model_1 | I(q)

6c12__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (8 domains)

CATH v4.4 (2 domains)

7. Citations (1)

SDHA-SDHE complex

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

Succinate dehydrogenase flavoprotein subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

FAD assembly factor SdhE

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

6c12__assembly_1__model_1

6c12__assembly_1__model_1 | I(q)

6c12__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (8 domains)

CATH v4.4 (2 domains)

7. Citations (1)