2eq9

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb

Method: X-RAY DIFFRACTION

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

Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component × 1 （Q5SLR1） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component × 1 （Q5SLR1） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component × 1 （Q5SLR1） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component × 1 （Q5SLR1） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SLR0_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–464； UniProt 1–464 Author chain B； PDBConstruct 1–464； UniProt 1–464 Author chain D； PDBConstruct 1–464； UniProt 1–464 Author chain E； PDBConstruct 1–464； UniProt 1–464 Author chain G； PDBConstruct 1–464； UniProt 1–464 Author chain H； PDBConstruct 1–464； UniProt 1–464 Author chain J； PDBConstruct 1–464； UniProt 1–464 Author chain K； PDBConstruct 1–464； UniProt 1–464

Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component

Thermus thermophilus

UniProt Q5SLR1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component × 2 （Q5SLR0） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component × 2 （Q5SLR0） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component × 2 （Q5SLR0） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component × 2 （Q5SLR0） FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SLR1_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–41； UniProt 146–185 Author chain F； PDBConstruct 2–41； UniProt 146–185 Author chain I； PDBConstruct 2–41； UniProt 146–185 Author chain L； PDBConstruct 2–41； UniProt 146–185

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	2eq9
Deposition date deposition_date	2007-03-30
Structure title title	Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb
Keywords keywords	;PROTEIN-PROTEIN COMPLEX, OXIDOREDUCTASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

2eq9__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2eq9__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2eq9__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	30.40 Å
Rg (electron density)	29.61 Å
Total Rg	30.30 Å
Atom count	7202
Residues	960
Excluded volume	129240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2eq9__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2eq9__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2eq9__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2eq9__assembly_4__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component
Molecular weight formula_weight	49151.8 kDa
EC 编号 ec_number	1.8.1.4
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E,G,H,J,K
Atom count atom_count	29827

MTPMKTYDLIVIGTGPGGYHAAIRAAQLGLKVLAVEAGEVGGVCLNVGCIPTKALLHAAETLHHLKVAEGFGLKAKPELDLKKLGGWRDQVVKKLTGGVGTLLKGNGVELLRGFARLVGPKEVEVGGERYGAKSLILATGSEPLELKGFPFGEDVWDSTRALKVEEGLPKRLLVIGGGAVGLELGQVYRRLGAEVTLIEYMPEILPQGDPETAALLRRALEKEGIRVRTKTKAVGYEKKKDGLHVRLEPAEGGEGEEVVVDKVLVAVGRKPRTEGLGLEKAGVKVDERGFIRVNARMETSVPGVYAIGDAARPPLLAHKAMREGLIAAENAAGKDSAFDYQVPSVVYTSPEWAGVGLTEEEAKRAGYKVKVGKFPLAASGRALTLGGAEGMVKVVGDEETDLLLGVFIVGPQAGELIAEAALALEMGATLTDLALTVHPHPTLSESLMEAAEAFHKQAIHILNR

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component
Molecular weight formula_weight	4450.2 kDa
EC 编号 ec_number	2.3.1.168
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

MLAVPAARKLARELGIPIEEVPGSGPLGRVRVEDVRAYAER

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
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	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1007

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2eq9c_
Class class	a — All alpha proteins
Fold Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family family	a.9.1.0 — automated matches

Domain ID domain_id	d2eq9f_
Class class	a — All alpha proteins
Fold Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family family	a.9.1.0 — automated matches

Domain ID domain_id	d2eq9i_
Class class	a — All alpha proteins
Fold Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family family	a.9.1.0 — automated matches

Domain ID domain_id	d2eq9l_
Class class	a — All alpha proteins
Fold Fold fold	a.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamily	a.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family family	a.9.1.0 — automated matches

CATH v4.4 (28 domains)

Domain ID domain_id	2eq9A01
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	2eq9A02
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	2eq9A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2eq9B01
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	2eq9B02
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	2eq9B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2eq9C00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

Domain ID domain_id	2eq9D01
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	2eq9D02
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	2eq9D03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2eq9E01
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	2eq9E02
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	2eq9E03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2eq9F00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

Domain ID domain_id	2eq9G01
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	2eq9G02
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	2eq9G03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2eq9H01
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	2eq9H02
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	2eq9H03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2eq9I00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

Domain ID domain_id	2eq9J01
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	2eq9J02
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	2eq9J03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2eq9K01
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	2eq9K02
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	2eq9K03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	30 — FAD/NAD-linked reductase, C-terminal dimerisation domain

Domain ID domain_id	2eq9L00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 — E3-binding domain

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Unit-cell length a length_a	88.781 Å
Unit-cell length b length_b	88.877 Å
Unit-cell length c length_c	144.149 Å
Unit-cell angle α angle_alpha	89.26 °
Unit-cell angle β angle_beta	87.01 °
Unit-cell angle γ angle_gamma	70.84 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	43.620 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2570

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb

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

Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component

State in the Current Structure

Other States of the Same Protein in the Database

Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component

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

2eq9__assembly_3__model_1

2eq9__assembly_3__model_1 | I(q)

2eq9__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (4 domains)

CATH v4.4 (28 domains)

7. Citations (1)

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb

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

Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component

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

2eq9__assembly_3__model_1

2eq9__assembly_3__model_1 | I(q)

2eq9__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (4 domains)

CATH v4.4 (28 domains)

7. Citations (1)