← Back to search
3exh

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex

Method: X-RAY DIFFRACTION
▼

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

Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

Homo sapiens

UniProt P08559

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Pyruvate dehydrogenase E1 component subunit beta, mitochondrial × 2 （P11177） MANGANESE (II) ION × 2 POTASSIUM ION × 2 THIAMINE DIPHOSPHATE × 2 GLYCEROL × 3 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Pyruvate dehydrogenase E1 component subunit beta, mitochondrial × 2 （P11177） MANGANESE (II) ION × 2 POTASSIUM ION × 2 THIAMINE DIPHOSPHATE × 2 GLYCEROL × 2 water × 4 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
1ni4 2ozl 3exe 3exe 3exf 3exf 3exg 3exg 3exg 3exg 3exg 3exg

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ODPA_HUMAN
Isoform —
PDB entities 1, 3
Chains and sequence ranges Author chain A； PDBConstruct 22–382； UniProt 30–390 Author chain E； PDBConstruct 22–382； UniProt 30–390 Author chain C； PDBConstruct 22–382； UniProt 30–390 Author chain G； PDBConstruct 22–382； UniProt 30–390

Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

Homo sapiens

UniProt P11177

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial × 1 （P08559） Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial × 1 （P08559） MANGANESE (II) ION × 2 POTASSIUM ION × 2 THIAMINE DIPHOSPHATE × 2 GLYCEROL × 3 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial × 1 （P08559） Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial × 1 （P08559） MANGANESE (II) ION × 2 POTASSIUM ION × 2 THIAMINE DIPHOSPHATE × 2 GLYCEROL × 2 water × 4 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
1ni4 2ozl 3exe 3exe 3exf 3exf 3exg 3exg 3exg 3exg 3exg 3exg

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ODPB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–329； UniProt 31–359 Author chain D； PDBConstruct 1–329； UniProt 31–359 Author chain F； PDBConstruct 1–329； UniProt 31–359 Author chain H； PDBConstruct 1–329； UniProt 31–359

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3exh
Deposition date deposition_date2008-10-16
Structure title titleCrystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex
Keywords keywords;heterotetramer; thiamine diphosphate-dependent enzyme; Disease mutation; Glycolysis; Leigh syndrome; Mitochondrion; Oxidoreductase; Phosphoprotein; Alternative splicing; Polymorphism; Pyruvate; Thiamine pyrophosphate; Transit peptide, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

3exh__assembly_1__model_1

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

Download this curve (.dat)

3exh__assembly_1__model_1 | I(q)

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

3exh__assembly_1__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）32.53 Å
Rg (electron density)31.75 Å
Total Rg32.40 Å
Atom count10739
Residues1378
Excluded volume191300 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3exh__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3exh__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

▼

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd3exha1
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_idd3exha2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3exhb1
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_idd3exhb2
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.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
Domain ID domain_idd3exhc1
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_idd3exhc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3exhd1
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_idd3exhd2
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.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
Domain ID domain_idd3exhe1
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_idd3exhe2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3exhf1
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_idd3exhf2
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.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
Domain ID domain_idd3exhg1
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_idd3exhg2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3exhh1
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_idd3exhh2
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.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

CATH v4.4 (12 domains)

Domain ID domain_id3exhA00
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_id3exhB01
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_id3exhB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id3exhC00
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_id3exhD01
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_id3exhD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id3exhE00
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_id3exhF01
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_id3exhF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id3exhG00
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_id3exhH01
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_id3exhH02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
▶

7. Citations (1)