2acz

Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site

Method: X-RAY DIFFRACTION

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

Succinate dehydrogenase flavoprotein subunit

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Succinate dehydrogenase iron-sulfur protein × 3 （P07014） Succinate dehydrogenase cytochrome b556 subunit × 3 （P69054） Succinate dehydrogenase hydrophobic membrane anchor protein × 3 （P10445） OXALOACETATE ION × 3 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 3 IRON/SULFUR CLUSTER × 3 FE3-S4 CLUSTER × 3 HEME B/C × 3 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE × 3 CARDIOLIPIN × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

Succinate dehydrogenase iron-sulfur protein

Escherichia coli

UniProt P07014

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Succinate dehydrogenase flavoprotein subunit × 3 （P10444） Succinate dehydrogenase cytochrome b556 subunit × 3 （P69054） Succinate dehydrogenase hydrophobic membrane anchor protein × 3 （P10445） OXALOACETATE ION × 3 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 3 IRON/SULFUR CLUSTER × 3 FE3-S4 CLUSTER × 3 HEME B/C × 3 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE × 3 CARDIOLIPIN × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHSB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–238； UniProt 1–238

Succinate dehydrogenase cytochrome b556 subunit

Escherichia coli

UniProt P69054

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Succinate dehydrogenase flavoprotein subunit × 3 （P10444） Succinate dehydrogenase iron-sulfur protein × 3 （P07014） Succinate dehydrogenase hydrophobic membrane anchor protein × 3 （P10445） OXALOACETATE ION × 3 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 3 IRON/SULFUR CLUSTER × 3 FE3-S4 CLUSTER × 3 HEME B/C × 3 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE × 3 CARDIOLIPIN × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHSC_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–129； UniProt 1–129

Succinate dehydrogenase hydrophobic membrane anchor protein

Escherichia coli

UniProt P10445

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Succinate dehydrogenase flavoprotein subunit × 3 （P10444） Succinate dehydrogenase iron-sulfur protein × 3 （P07014） Succinate dehydrogenase cytochrome b556 subunit × 3 （P69054） OXALOACETATE ION × 3 FLAVIN-ADENINE DINUCLEOTIDE × 3 FE2/S2 (INORGANIC) CLUSTER × 3 IRON/SULFUR CLUSTER × 3 FE3-S4 CLUSTER × 3 HEME B/C × 3 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE × 3 CARDIOLIPIN × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHSD_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–115； UniProt 1–115

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	2acz
Deposition date deposition_date	2005-07-19
Structure title title	Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site
Keywords keywords	;MEMBRANE PROTEIN, Aerobic reparatory Complex II, SQR, succinate:ubiquinone oxidoreductase, AA5, AT5, Atpenin A5, SDH, succinate dehydrogenase, Oxidoreductase-Electron transport COMPLEX ;; Oxidoreductase/Electron transport
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.

2acz__assembly_1__model_1

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

Download this curve (.dat)

2acz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2acz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.47 Å
Rg (electron density)	46.06 Å
Total Rg	46.19 Å
Atom count	25563
Residues	3204
Excluded volume	457440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2acz__assembly_1__model_1`	dodecameric （12）	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 flavoprotein subunit
Molecular weight formula_weight	64502.8 kDa
EC 编号 ec_number	1.3.99.1
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	8521

MKLPVREFDAVVIGAGGAGMRAALQISQSGQTCALLSKVFPTRSHTVSAQGGITVALGNTHEDNWEWHMYDTVKGSDYIGDQDAIEYMCKTGPEAILELEHMGLPFSRLDDGRIYQRPFGGQSKNFGGEQAARTAAAADRTGHALLHTLYQQNLKNHTTIFSEWYALDLVKNQDGAVVGCTALCIETGEVVYFKARATVLATGGAGRIYQSTTNAHINTGDGVGMAIRAGVPVQDMEMWQFHPTGIAGAGVLVTEGCRGEGGYLLNKHGERFMERYAPNAKDLAGRDVVARSIMIEIREGRGCDGPWGPHAKLKLDHLGKEVLESRLPGILELSRTFAHVDPVKEPIPVIPTCHYMMGGIPTKVTGQALTVNEKGEDVVVPGLFAVGEIACVSVHGANRLGGNSLLDLVVFGRAAGLHLQESIAEQGALRDASESDVEASLDRLNRWNNNRNGEDPVAIRKALQECMQHNFSVFREGDAMAKGLEQLKVIRERLKNARLDDTSSEFNTQRVECLELDNLMETAYATAVSANFRTESRGAHSRFDFPDRDDENWLCHSLYLPESESMTRRSVNMEPKLRPAFPPKIRTY

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Succinate dehydrogenase iron-sulfur protein
Molecular weight formula_weight	26800.9 kDa
EC 编号 ec_number	1.3.99.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRLEFSIYRYNPDVDDAPRMQDYTLEADEGRDMMLLDALIQLKEKDPSLSFRRSCREGVCGSDGLNMNGKNGLACITPISALNQPGKKIVIRPLPGLPVIRDLVVDMGQFYAQYEKIKPYLLNNGQNPPAREHLQMPEQREKLDGLYECILCACCSTSCPSFWWNPDKFIGPAGLLAAYRFLIDSRDTETDSRLDGLSDAFSVFRCHSIMNCVSVCPKGLNPTRAIGHIKSMLLQRNA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Succinate dehydrogenase cytochrome b556 subunit
Molecular weight formula_weight	14313.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MIRNVKKQRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQASAIMGSFFVKFIMWGILTALAYHVVVGIRHMMMDFGYLEETFEAGKRSAKISFVITVVLSLLAGVLVW

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Succinate dehydrogenase hydrophobic membrane anchor protein
Molecular weight formula_weight	12874.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MVSNASALGRNGVHDFILVRATAIVLTLYIIYMVGFFATSGELTYEVWIGFFASAFTKVFTLLALFSILIHAWIGMWQVLTDYVKPLALRLMLQLVIVVALVVYVIYGFVVVWGV

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 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 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	HEME B/C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE
Molecular weight formula_weight	366.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	CARDIOLIPIN
Molecular weight formula_weight	1151.5 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2aczb1
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	d2aczb2
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	d2aczc_
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	d2aczd1
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 (8 domains)

Domain ID domain_id	2aczA01
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	2aczA02
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	2aczA03
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	2aczA04
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	2aczB01
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	2aczB02
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	2aczC00
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	2aczD01
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	138.759 Å
Unit-cell length b length_b	138.759 Å
Unit-cell length c length_c	521.873 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2640
R_free r_free	0.3080

Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site

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

Succinate dehydrogenase iron-sulfur protein

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 b556 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

Succinate dehydrogenase hydrophobic membrane anchor protein

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

2acz__assembly_1__model_1

2acz__assembly_1__model_1 | I(q)

2acz__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

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 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)