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1kkq

Crystal structure of the human PPAR-alpha ligand-binding domain in complex with an antagonist GW6471 and a SMRT corepressor motif

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

PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR

Homo sapiens

UniProt Q07869

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 NUCLEAR RECEPTOR CO-REPRESSOR 2 × 1 （Q9Y618） ;N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE ; × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 NUCLEAR RECEPTOR CO-REPRESSOR 2 × 1 （Q9Y618） ;N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE ; × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 NUCLEAR RECEPTOR CO-REPRESSOR 2 × 1 （Q9Y618） ;N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE ; × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 NUCLEAR RECEPTOR CO-REPRESSOR 2 × 1 （Q9Y618） ;N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE ; × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1i7g 2rew 2znn 3kdt 3kdt 3kdu 3kdu 3vi8 4bcr 4bcr 4ci4 5azt

52 assemblies; showing the first 12

Homodimer
3kdt 3kdu 7e5f 7e5g 7e5h 7e5i

6 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1k7l 1k7l 1k7l 1k7l 1kkq 1kkq 1kkq 1kkq 2npa 2npa 2p54 3et1

49 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PPAR_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–269； UniProt 200–468 Author chain B； PDBConstruct 1–269； UniProt 200–468 Author chain C； PDBConstruct 1–269； UniProt 200–468 Author chain D； PDBConstruct 1–269； UniProt 200–468

NUCLEAR RECEPTOR CO-REPRESSOR 2

OrganismNot specified

UniProt Q9Y618

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR × 1 （Q07869） ;N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE ; × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR × 1 （Q07869） ;N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE ; × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR × 1 （Q07869） ;N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE ; × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR × 1 （Q07869） ;N-((2S)-2-({(1Z)-1-METHYL-3-OXO-3-[4-(TRIFLUOROMETHYL) PHENYL]PROP-1-ENYL}AMINO)-3-{4-[2-(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)ETHOXY]PHENYL}PROPYL)PROPANAMIDE ; × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1xc5 2ltp

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1kkq 1kkq 1kkq 1kkq 1r2b 2gpv 2gpv 2rt5 3r29 3r2a 4a69 4a69

70 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NCOR2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–19； UniProt 2339–2357 Author chain F； PDBConstruct 1–19； UniProt 2339–2357 Author chain G； PDBConstruct 1–19； UniProt 2339–2357 Author chain H； PDBConstruct 1–19； UniProt 2339–2357

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_id1kkq
Deposition date deposition_date2001-12-10
Structure title titleCrystal structure of the human PPAR-alpha ligand-binding domain in complex with an antagonist GW6471 and a SMRT corepressor motif
Keywords keywordsnuclear corepressor nuclear hormone receptors antagonist, TRANSCRIPTION; TRANSCRIPTION
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.

1kkq__assembly_1__model_1

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

Download this curve (.dat)

1kkq__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1kkq__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）20.66 Å
Rg (electron density)19.41 Å
Total Rg20.35 Å
Atom count2318
Residues288
Excluded volume41924 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1kkq__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1kkq__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1kkq__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1kkq__assembly_4__model_1 dimeric （2） 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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1kkqa_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain
Domain ID domain_idd1kkqb_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain
Domain ID domain_idd1kkqc_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain
Domain ID domain_idd1kkqd_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (4 domains)

Domain ID domain_id1kkqA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id1kkqB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id1kkqC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id1kkqD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
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7. Citations (2)