SAXSdb — 9h2i

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

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyl dehydrogenase × 2 （P0A9P0） 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	ODP2_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–66； UniProt 315–380

Dihydrolipoyl dehydrogenase

Escherichia coli

UniProt P0A9P0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P06959） 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	DLDH_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–473； UniProt 2–474 Author chain C； PDBConstruct 1–473； UniProt 2–474

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	9h2i
Deposition date deposition_date	2024-10-11
Last revision last_revision	2025-10-29
Structure title title	Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate dehydrogenase complex
Keywords keywords	complex, pyruvate dehydrogenase, electrostatic binding, FLAVOPROTEIN; FLAVOPROTEIN
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.

9h2i__assembly_1__model_1

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

Download this curve (.dat)

9h2i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9h2i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.02 Å
Rg (electron density)	30.15 Å
Total Rg	30.80 Å
Atom count	7565
Residues	990
Excluded volume	135380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9h2i__assembly_1__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	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Molecular weight formula_weight	7210.2 kDa
EC 编号 ec_number	2.3.1.12
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	8146

EGKSEFAENDAYVHATPLIRRLAREFGVNLAKVKGTGRKGRILREDVQAYVKEAIKRAEAAPAATG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Dihydrolipoyl dehydrogenase
Molecular weight formula_weight	50624.2 kDa
EC 编号 ec_number	1.8.1.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

STEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLVMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTAVEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWVGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	581

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Unit-cell length a length_a	60.703 Å
Unit-cell length b length_b	88.353 Å
Unit-cell length c length_c	200.687 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	orthorhombic

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	36.860 Å
R factor r_factor	0.1919
R_work r_work	0.1898
R_free r_free	0.2307

Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate dehydrogenase complex

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

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

State in the Current Structure

Other States of the Same Protein in the Database

Dihydrolipoyl dehydrogenase

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

9h2i__assembly_1__model_1

9h2i__assembly_1__model_1 | I(q)

9h2i__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 (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

7. Citations (1)

Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate dehydrogenase complex

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

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Dihydrolipoyl dehydrogenase

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

9h2i__assembly_1__model_1

9h2i__assembly_1__model_1 | I(q)

9h2i__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 (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

7. Citations (1)