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3dva

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pyruvate dehydrogenase E1 component subunit alpha

Bacillus stearothermophilus

UniProt P21873

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 POTASSIUM ION × 2 water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1w85 1w85 1w88 1w88 3duf 3duf 3dv0 3dv0 3dva 3dva

10 assemblies

View Construct and Data Evidence
UniProt name ODPA_BACST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–369； UniProt 1–369 Author chain C； PDBConstruct 1–369； UniProt 1–369 Author chain E； PDBConstruct 1–369； UniProt 1–369 Author chain G； PDBConstruct 1–369； UniProt 1–369

Pyruvate dehydrogenase E1 component subunit beta

Bacillus stearothermophilus

UniProt P21874

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 POTASSIUM ION × 2 water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P11961） MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1w85 1w85 1w88 1w88 3duf 3duf 3dv0 3dv0 3dva 3dva

10 assemblies

View Construct and Data Evidence
UniProt name ODPB_BACST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–325； UniProt 1–325 Author chain D； PDBConstruct 1–325； UniProt 1–325 Author chain F； PDBConstruct 1–325； UniProt 1–325 Author chain H； PDBConstruct 1–325； UniProt 1–325

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

Bacillus stearothermophilus

UniProt P11961

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 POTASSIUM ION × 2 water × 5 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Pyruvate dehydrogenase E1 component subunit alpha × 2 （P21873） Pyruvate dehydrogenase E1 component subunit beta × 2 （P21874） MAGNESIUM ION × 3 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 2 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1lab 1lac 1w3d 1w4e 1w4f 1w4g 1w4h 2pdd 2pde

9 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
1b5s 9ukz

2 assemblies

Heteromeric or nucleic-acid complex
1ebd 1w85 1w85 1w88 1w88 3duf 3duf 3dv0 3dv0 3dva 3dva

11 assemblies

View Construct and Data Evidence
UniProt name ODP2_BACST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain I； PDBConstruct 1–428； UniProt 1–428 Author chain J； PDBConstruct 1–428； UniProt 1–428

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_id3dva
Deposition date deposition_date2008-07-18
Structure title titleSnapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
Keywords keywords;Oxidoreductase, PYRUVATE, DEHYDROGENASE, DIHYDROLIPOYL, ACETYL TRANSFERASE, MULTIENZYME COMPLEX, TRANSFERASE, Glycolysis, Phosphoprotein, Thiamine pyrophosphate, Acyltransferase, OXIDOREDUCTASE-TRANSFERASE COMPLEX ;; OXIDOREDUCTASE/TRANSFERASE
Experimental Method methodX-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.

3dva__assembly_2__model_1

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

Download this curve (.dat)

3dva__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3dva__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）33.25 Å
Rg (electron density)32.26 Å
Total Rg32.94 Å
Atom count11018
Residues1407
Excluded volume196740 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3dva__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3dva__assembly_2__model_1 pentameric （5） 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 (7)

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (14 domains)

Domain ID domain_idd3dvaa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module
Domain ID domain_idd3dvab1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd3dvab2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.0 — automated matches
Domain ID domain_idd3dvac_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module
Domain ID domain_idd3dvad1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd3dvad2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.0 — automated matches
Domain ID domain_idd3dvae_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module
Domain ID domain_idd3dvaf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd3dvaf2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.0 — automated matches
Domain ID domain_idd3dvag_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module
Domain ID domain_idd3dvah1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd3dvah2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.0 — automated matches
Domain ID domain_idd3dvai_
Class classa — All alpha proteins
Fold Fold folda.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamilya.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family familya.9.1.0 — automated matches
Domain ID domain_idd3dvaj_
Class classa — All alpha proteins
Fold Fold folda.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamilya.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family familya.9.1.0 — automated matches

CATH v4.4 (14 domains)

Domain ID domain_id3dvaA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id3dvaB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id3dvaB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id3dvaC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id3dvaD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id3dvaD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id3dvaE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id3dvaF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id3dvaF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id3dvaG00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id3dvaH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id3dvaH02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id3dvaI00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily10 — E3-binding domain
Domain ID domain_id3dvaJ00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology320 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily10 — E3-binding domain
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7. Citations (1)