3sfe

crystal structure of porcine mitochondrial respiratory complex II bound with oxaloacetate and thiabendazole

Method: X-RAY DIFFRACTION

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

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial × 1 （Q007T0） Succinate dehydrogenase cytochrome b560 subunit, mitochondrial × 1 （D0VWV4） Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial × 1 （A5GZW8） FLAVIN-ADENINE DINUCLEOTIDE × 1 OXALOACETATE ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-(1,3-THIAZOL-4-YL)-1H-BENZIMIDAZOLE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHSA_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–622； UniProt 43–664

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

OrganismNot specified

UniProt Q007T0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （Q0QF01） Succinate dehydrogenase cytochrome b560 subunit, mitochondrial × 1 （D0VWV4） Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial × 1 （A5GZW8） FLAVIN-ADENINE DINUCLEOTIDE × 1 OXALOACETATE ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-(1,3-THIAZOL-4-YL)-1H-BENZIMIDAZOLE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHSB_PIG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–252； UniProt 29–280

Succinate dehydrogenase cytochrome b560 subunit, mitochondrial

OrganismNot specified

UniProt D0VWV4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （Q0QF01） Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial × 1 （Q007T0） Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial × 1 （A5GZW8） FLAVIN-ADENINE DINUCLEOTIDE × 1 OXALOACETATE ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-(1,3-THIAZOL-4-YL)-1H-BENZIMIDAZOLE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C560_PIG
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–140； UniProt 30–169

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

OrganismNot specified

UniProt A5GZW8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （Q0QF01） Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial × 1 （Q007T0） Succinate dehydrogenase cytochrome b560 subunit, mitochondrial × 1 （D0VWV4） FLAVIN-ADENINE DINUCLEOTIDE × 1 OXALOACETATE ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-(1,3-THIAZOL-4-YL)-1H-BENZIMIDAZOLE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHSD_PIG
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–103； UniProt 57–159

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	3sfe
Deposition date deposition_date	2011-06-13
Structure title title	crystal structure of porcine mitochondrial respiratory complex II bound with oxaloacetate and thiabendazole
Keywords keywords	succinate:ubiquinone oxidoreductase, thiabendazole, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

3sfe__assembly_1__model_1

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

Download this curve (.dat)

3sfe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3sfe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.56 Å
Rg (electron density)	33.04 Å
Total Rg	33.24 Å
Atom count	8627
Residues	1094
Excluded volume	153560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3sfe__assembly_1__model_1`	tetrameric （4）	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 (12)

Entity 1 Entity 1 polymer

Description description	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Molecular weight formula_weight	68313.2 kDa
EC 编号 ec_number	1.3.5.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8687

SSAKVSDAISTQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEEDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPASVVELENYGMPFSRTEDGKIYQRAFGGQSLKFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGSIHRIRARNTVVATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQDLEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTLEIREGRGCGPEKDHVYLQLHHLPPEQLAVRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNYKGQVLRHVNGQDQVVPGLYACGEAACASVHGANRLGANSLLDLVVFGRACALSIAESCRPGDKVPSIKPNAGEESVMNLDKLRFANGTIRTSELRLSMQKSMQSHAAVFRVGSVLQEGCEKILRLYGDLQHLKTFDRGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDFKERVDEYDYSKPIQGQQKKPFQEHWRKHTLSYVDVKTGKVSLEYRPVIDKTLNEADCATVPPAIRSY

Entity 2 Entity 2 polymer

Description description	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Molecular weight formula_weight	28792.3 kDa
EC 编号 ec_number	1.3.5.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AQTAAATAPRIKKFAIYRWDPDKTGDKPHMQTYEIDLNNCGPMVLDALIKIKNEIDSTLTFRRSCREGICGSCAMNINGGNTLACTRRIDTNLDKVSKIYPLPHMYVIKDLVPDLSNFYAQYKSIEPYLKKKDESQEGKQQYLQSIEEREKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWMIDSRDDFTEERLAKLQDPFSLYRCHTIMNCTGTCPKGLNPGKAIAEIKKMMATYKEKKASV

Entity 3 Entity 3 polymer

Description description	Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
Molecular weight formula_weight	15304.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

LGTTAKEEMERFWNKNLGSNRPLSPHITIYRWSLPMAMSICHRGTGIALSAGVSLFGLSALLLPGNFESHLELVKSLCLGPTLIYTAKFGIVFPLMYHTWNGIRHLIWDLGKGLTIPQLTQSGVVVLILTVLSSVGLAAM

Entity 4 Entity 4 polymer

Description description	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
Molecular weight formula_weight	10936.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

ASSKAASLHWTGERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGIGQVVTDYVRGDALQKAAKAGLLALSAFTFAGLCYFNYHDVGICKAVAMLWKL

Entity 5 Entity 5 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	OXALOACETATE ION
Molecular weight formula_weight	131.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	2-(1,3-THIAZOL-4-YL)-1H-BENZIMIDAZOLE
Molecular weight formula_weight	201.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	52

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d3sfea1
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	d3sfea2
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	d3sfea3
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	d3sfeb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins

Domain ID domain_id	d3sfeb2
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.2 — alpha-helical ferredoxin
Family Family family	a.1.2.1 — Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain

Domain ID domain_id	d3sfec_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.21 — Heme-binding four-helical bundle
Superfamily Superfamily superfamily	f.21.2 — Fumarate reductase respiratory complex transmembrane subunits
Family Family family	f.21.2.2 — Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)

Domain ID domain_id	d3sfed_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.21 — Heme-binding four-helical bundle
Superfamily Superfamily superfamily	f.21.2 — Fumarate reductase respiratory complex transmembrane subunits
Family Family family	f.21.2.2 — Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)

CATH v4.4 (9 domains)

Domain ID domain_id	3sfeA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3sfeA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	3sfeA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	100 — Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain

Domain ID domain_id	3sfeA04
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	40 — succinate dehydrogenase protein domain

Domain ID domain_id	3sfeB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

Domain ID domain_id	3sfeB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1060 — Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
Homologous superfamily homologous superfamily	10 — Alpha-helical ferredoxin

Domain ID domain_id	3sfeC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	540 — Single helix bin

Domain ID domain_id	3sfeC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	10 — Fumarate reductase/succinate dehydrogenase, transmembrane subunit

Domain ID domain_id	3sfeD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily	10 — Fumarate reductase/succinate dehydrogenase, transmembrane subunit

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Unit-cell length a length_a	70.710 Å
Unit-cell length b length_b	83.420 Å
Unit-cell length c length_c	294.010 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	4

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

Resolution resolution	2.810 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2168
R_work r_work	0.2140
R_free r_free	0.2698

crystal structure of porcine mitochondrial respiratory complex II bound with oxaloacetate and thiabendazole

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

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, 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 dehydrogenase [ubiquinone] iron-sulfur subunit, 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 dehydrogenase cytochrome b560 subunit, 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 dehydrogenase [ubiquinone] cytochrome b small subunit, 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

3sfe__assembly_1__model_1

3sfe__assembly_1__model_1 | I(q)

3sfe__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer 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 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (7 domains)

CATH v4.4 (9 domains)

7. Citations (1)