3p4r

Crystal structure of Menaquinol:fumarate oxidoreductase in complex with glutarate

Method: X-RAY DIFFRACTION

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

Fumarate reductase flavoprotein subunit

Escherichia coli 042

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase iron-sulfur subunit × 1 （D3GV55） Fumarate reductase subunit C × 1 （D3QL74） Fumarate reductase subunit D × 1 （D3GV53） FLAVIN-ADENINE DINUCLEOTIDE × 1 GLUTARIC ACID × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase iron-sulfur subunit × 1 （D3GV55） Fumarate reductase subunit C × 1 （D3QL74） Fumarate reductase subunit D × 1 （D3GV53） FLAVIN-ADENINE DINUCLEOTIDE × 1 GLUTARIC ACID × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3GV56_ECO44
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–577； UniProt 1–577 Author chain M； PDBConstruct 1–577； UniProt 1–577

Fumarate reductase iron-sulfur subunit

Escherichia coli 042

UniProt D3GV55

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （D3GV56） Fumarate reductase subunit C × 1 （D3QL74） Fumarate reductase subunit D × 1 （D3GV53） FLAVIN-ADENINE DINUCLEOTIDE × 1 GLUTARIC ACID × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （D3GV56） Fumarate reductase subunit C × 1 （D3QL74） Fumarate reductase subunit D × 1 （D3GV53） FLAVIN-ADENINE DINUCLEOTIDE × 1 GLUTARIC ACID × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3GV55_ECO44
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–243； UniProt 2–244 Author chain N； PDBConstruct 1–243； UniProt 2–244

Fumarate reductase subunit C

Escherichia coli O55:H7

UniProt D3QL74

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （D3GV56） Fumarate reductase iron-sulfur subunit × 1 （D3GV55） Fumarate reductase subunit D × 1 （D3GV53） FLAVIN-ADENINE DINUCLEOTIDE × 1 GLUTARIC ACID × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （D3GV56） Fumarate reductase iron-sulfur subunit × 1 （D3GV55） Fumarate reductase subunit D × 1 （D3GV53） FLAVIN-ADENINE DINUCLEOTIDE × 1 GLUTARIC ACID × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3QL74_ECOCB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–130； UniProt 2–131 Author chain O； PDBConstruct 1–130； UniProt 2–131

Fumarate reductase subunit D

Escherichia coli 042

UniProt D3GV53

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （D3GV56） Fumarate reductase iron-sulfur subunit × 1 （D3GV55） Fumarate reductase subunit C × 1 （D3QL74） FLAVIN-ADENINE DINUCLEOTIDE × 1 GLUTARIC ACID × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Fumarate reductase flavoprotein subunit × 1 （D3GV56） Fumarate reductase iron-sulfur subunit × 1 （D3GV55） Fumarate reductase subunit C × 1 （D3QL74） FLAVIN-ADENINE DINUCLEOTIDE × 1 GLUTARIC ACID × 1 FE2/S2 (INORGANIC) CLUSTER × 1 FE3-S4 CLUSTER × 1 IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3GV53_ECO44
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–119； UniProt 1–119 Author chain P； PDBConstruct 1–119； UniProt 1–119

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	3p4r
Deposition date deposition_date	2010-10-07
Structure title title	Crystal structure of Menaquinol:fumarate oxidoreductase in complex with glutarate
Keywords keywords	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.

3p4r__assembly_1__model_1

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

Download this curve (.dat)

3p4r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3p4r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.39 Å
Rg (electron density)	33.04 Å
Total Rg	33.14 Å
Atom count	8402
Residues	1069
Excluded volume	150000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3p4r__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3p4r__assembly_2__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 (9)

Entity 1 Entity 1 polymer

Description description	Fumarate reductase flavoprotein subunit
Molecular weight formula_weight	63477.7 kDa
EC 编号 ec_number	1.3.99.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,M
Atom count atom_count	16804

MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDHDSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGMKIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGTLVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGSGILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWRKGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMGGIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGNGNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKLAELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGCTERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPA

Source Source

Source organism organism	Escherichia coli 042
NCBI taxonomy ID ncbi_taxonomy_id	216592
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Fumarate reductase iron-sulfur subunit
Molecular weight formula_weight	27021.9 kDa
EC 编号 ec_number	1.3.99.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,N

AEMKNLKIEVVRYNPEVDTAPHSAFYEVPYDATTSLLDALGYIKDNLAPDLSYRWSCRMAICGSCGMMVNNVPKLACKTFLRDYTDGMKVEALANFPIERDLVVDMTHFIESLEAIKPYIIGNSRTADQGTNIQTPAQMAKYHQFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHVDPAAAIQQGKVESSKDFLIATLKPR

Source Source

Source organism organism	Escherichia coli 042
NCBI taxonomy ID ncbi_taxonomy_id	216592
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Fumarate reductase subunit C
Molecular weight formula_weight	14898.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TTKRKPYVRPMTSTWWKKLPFYRFYMLREGTAVPAVWFSIELIFGLFALKNGPEAWAGFVDFLQNPVIVIINLITLAAALLHTKTWFELAPKAANIIVKDEKMGPEPIIKSLWAVTVVATIVILFVALYW

Source Source

Source organism organism	Escherichia coli O55:H7
NCBI taxonomy ID ncbi_taxonomy_id	701177
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Fumarate reductase subunit D
Molecular weight formula_weight	13118.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MINPNPKRSDEPVFWGLFGAGGMWSAIIAPVMILLVGILLPLGLFPGDALSYERVLAFAQSFIGRVFLFLMIVLPLWCGLHRMHHAMHDLKIHVPAGKWVFYGLAAILTVVTLIGVVTI

Source Source

Source organism organism	Escherichia coli 042
NCBI taxonomy ID ncbi_taxonomy_id	216592
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	2

Entity 6 Entity 6 non-polymer

Description description	GLUTARIC ACID
Molecular weight formula_weight	132.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 8 Entity 8 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3p4rb1
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	d3p4rb2
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	d3p4rc_
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	d3p4rn1
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	d3p4rn2
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	d3p4ro_
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 (16 domains)

Domain ID domain_id	3p4rA01
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	3p4rA02
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	3p4rA03
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	3p4rA04
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	3p4rB01
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	3p4rB02
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	3p4rC00
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	3p4rD00
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	3p4rM01
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	3p4rM02
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	3p4rM03
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	3p4rM04
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	3p4rN01
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	3p4rN02
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	3p4rO00
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	3p4rP00
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	96.678 Å
Unit-cell length b length_b	138.016 Å
Unit-cell length c length_c	269.558 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	3.050 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2490
R_work r_work	0.2480
R_free r_free	0.2840

Crystal structure of Menaquinol:fumarate oxidoreductase in complex with glutarate

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

Fumarate reductase 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

Fumarate reductase 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

Fumarate reductase subunit C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fumarate reductase subunit D

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

3p4r__assembly_1__model_1

3p4r__assembly_1__model_1 | I(q)

3p4r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (9)

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

6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (6 domains)

CATH v4.4 (16 domains)

7. Citations (1)