2wu5

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD His71Met mutant

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 4	SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	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 Author chain E； PDBConstruct 1–588； UniProt 1–588 Author chain I； PDBConstruct 1–588； UniProt 1–588

SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT

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 4	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	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 Author chain F； PDBConstruct 1–238； UniProt 1–238 Author chain J； 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 4	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT × 1 （P0AC44） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	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 Author chain G； PDBConstruct 1–129； UniProt 1–129 Author chain K； PDBConstruct 1–129； UniProt 1–129

SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN SUBUNIT

ESCHERICHIA COLI

UniProt P0AC44

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 FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT × 1 （P0AC41） SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT × 1 （P07014） SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT × 1 （P69054） FLAVIN-ADENINE DINUCLEOTIDE × 1 MALATE LIKE INTERMEDIATE × 1 SODIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE × 1 water × 4	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 Author chain H； PDBConstruct 1–115； UniProt 1–115 Author chain L； 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	2wu5
Deposition date deposition_date	2009-09-29
Structure title title	Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD His71Met mutant
Keywords keywords	;CELL INNER MEMBRANE, TRICARBOXYLIC ACID CYCLE, METAL-BINDING, TRANSMEMBRANE, TRANSPORT, FLAVOPROTEIN, OXIDOREDUCTASE, ELECTRON TRANSPORT ;; 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.

2wu5__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2wu5__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wu5__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	32.53 Å
Rg (electron density)	33.31 Å
Total Rg	33.35 Å
Atom count	8314
Residues	1053
Excluded volume	148470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wu5__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wu5__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2wu5__assembly_3__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 (13)

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, 1.3.99.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I
Atom count atom_count	25164

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 SUBUNIT
Molecular weight formula_weight	26800.9 kDa
EC 编号 ec_number	1.3.5.1, 1.3.99.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J

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
EC 编号 ec_number	1.3.5.1
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K

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 SUBUNIT
Molecular weight formula_weight	12867.5 kDa
EC 编号 ec_number	1.3.5.1
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MVSNASALGRNGVHDFILVRATAIVLTLYIIYMVGFFATSGELTYEVWIGFFASAFTKVFTLLALFSILIMAWIGMWQVLTDYVKPLALRLMLQLVIVVALVVYVIYGFVVVWGV

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	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MALATE LIKE INTERMEDIATE
Molecular weight formula_weight	132.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 11 Entity 11 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 12 Entity 12 non-polymer

Description description	2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
Molecular weight formula_weight	235.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	222

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6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d2wu5a1
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	d2wu5a2
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	d2wu5a3
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	d2wu5b1
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	d2wu5b2
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	d2wu5c_
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	d2wu5e1
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	d2wu5e2
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	d2wu5e3
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	d2wu5f1
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	d2wu5f2
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	d2wu5g_
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	d2wu5i1
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	d2wu5i2
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	d2wu5i3
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	d2wu5j1
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	d2wu5j2
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	d2wu5k_
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 (24 domains)

Domain ID domain_id	2wu5A01
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	2wu5A02
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	2wu5A03
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	2wu5A04
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	2wu5B01
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	2wu5B02
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	2wu5C00
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	2wu5D00
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	2wu5E01
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	2wu5E02
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	2wu5E03
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	2wu5E04
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	2wu5F01
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	2wu5F02
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	2wu5G00
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	2wu5H00
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	2wu5I01
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	2wu5I02
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	2wu5I03
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	2wu5I04
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	2wu5J01
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	2wu5J02
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	2wu5K00
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	2wu5L00
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

▶

Unit-cell length a length_a	120.060 Å
Unit-cell length b length_b	183.820 Å
Unit-cell length c length_c	203.420 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	12

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

Resolution resolution	2.803 Å
Low-resolution limit resolution_low	46.827 Å
R factor r_factor	0.2153
R_work r_work	0.2134
R_free r_free	0.2515

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD His71Met mutant

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 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 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 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2wu5__assembly_2__model_1

2wu5__assembly_2__model_1 | I(q)

2wu5__assembly_2__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 (13)

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

Entity 13 Entity 13 water

6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (18 domains)

CATH v4.4 (24 domains)

7. Citations (1)