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2pnr

Crystal Structure of the asymmetric Pdk3-l2 Complex

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

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3

Homo sapiens

UniProt Q15120

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 （P10515） DIHYDROLIPOIC ACID × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex × 1 （P10515） DIHYDROLIPOIC ACID × 1 water × 3 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
1y8n 1y8o 1y8p 2pnr 2pnr 2q8i

6 assemblies

View Construct and Data Evidence
UniProt name PDK3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–419； UniProt 9–406 Author chain B； PDBConstruct 22–419； UniProt 9–406 Author chain E； PDBConstruct 22–419； UniProt 9–406 Author chain F； PDBConstruct 22–419； UniProt 9–406

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

Homo sapiens

UniProt P10515

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 [lipoamide]] kinase isozyme 3 × 2 （Q15120） DIHYDROLIPOIC ACID × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 × 2 （Q15120） DIHYDROLIPOIC ACID × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1fyc 2dne 3b8k 6ct0 6ct0

5 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
6ct0 6ct0 6ct0 6h55 8piu

5 assemblies

Heteromeric or nucleic-acid complex
1y8n 1y8o 1y8p 2pnr 2pnr 2q8i 3crk 3crl

8 assemblies

View Construct and Data Evidence
UniProt name ODP2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 21–128； UniProt 179–286 Author chain G； PDBConstruct 21–128； UniProt 179–286

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_id2pnr
Deposition date deposition_date2007-04-25
Structure title titleCrystal Structure of the asymmetric Pdk3-l2 Complex
Keywords keywordspyruvate dehydrogenase kinase 3, lipoyl-bearing domain, asymmetric protein-protein complex, TRANSFERASE; 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.

2pnr__assembly_1__model_1

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

Download this curve (.dat)

2pnr__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.

2pnr__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）30.75 Å
Rg (electron density)29.87 Å
Total Rg30.69 Å
Atom count6440
Residues794
Excluded volume115460 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2pnr__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2pnr__assembly_2__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)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd2pnra1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Family Family familya.29.5.1 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Domain ID domain_idd2pnra3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamilyd.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family familyd.122.1.4 — alpha-ketoacid dehydrogenase kinase, C-terminal domain
Domain ID domain_idd2pnrb1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Family Family familya.29.5.1 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Domain ID domain_idd2pnrb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamilyd.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family familyd.122.1.4 — alpha-ketoacid dehydrogenase kinase, C-terminal domain
Domain ID domain_idd2pnrc_
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.1 — Single hybrid motif
Family Family familyb.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains
Domain ID domain_idd2pnre1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Family Family familya.29.5.1 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Domain ID domain_idd2pnre3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamilyd.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family familyd.122.1.4 — alpha-ketoacid dehydrogenase kinase, C-terminal domain
Domain ID domain_idd2pnrf1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.5 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Family Family familya.29.5.1 — alpha-ketoacid dehydrogenase kinase, N-terminal domain
Domain ID domain_idd2pnrf2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamilyd.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family familyd.122.1.4 — alpha-ketoacid dehydrogenase kinase, C-terminal domain
Domain ID domain_idd2pnrg_
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.1 — Single hybrid motif
Family Family familyb.84.1.1 — Biotinyl/lipoyl-carrier proteins and domains

CATH v4.4 (10 domains)

Domain ID domain_id2pnrA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily20 — Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain
Domain ID domain_id2pnrA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id2pnrB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily20 — Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain
Domain ID domain_id2pnrB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id2pnrC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
Domain ID domain_id2pnrE01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily20 — Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain
Domain ID domain_id2pnrE02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id2pnrF01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily20 — Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain
Domain ID domain_id2pnrF02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id2pnrG01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
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7. Citations (1)