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4wvd

Identification of a novel FXR ligand that regulates metabolism

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

Nuclear receptor corepressor 1

OrganismNot specified

UniProt O75376

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Bile acid receptor × 1 （Q96RI1） FORMIC ACID × 4 ;(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside ; × 1 water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Bile acid receptor × 1 （Q96RI1） FORMIC ACID × 4 ;(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside ; × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2eqr

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3h52 3h52 3kmz 3kmz 3kmz 3n00 3n00 4mdd 4wvd 4wvd 6wmq 6xxs

32 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NCOR1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–17； UniProt 2259–2275 Author chain D； PDBConstruct 1–17； UniProt 2259–2275

Bile acid receptor

Homo sapiens

UniProt Q96RI1

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 corepressor 1 × 1 （O75376） FORMIC ACID × 4 ;(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside ; × 1 water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Nuclear receptor corepressor 1 × 1 （O75376） FORMIC ACID × 4 ;(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside ; × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1osh 3fli 8hd3 8hd3

4 assemblies

Homodimer
4oiv

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3bej 3bej 3dct 3dcu 3gd2 3hc5 3hc6 3okh 3oki 3oki 3olf 3olf

132 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NR1H4_HUMAN
Isoform Q96RI1-2
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–211； UniProt 244–454 Author chain B； PDBConstruct 1–211； UniProt 244–454

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_id4wvd
Deposition date deposition_date2014-11-05
Structure title titleIdentification of a novel FXR ligand that regulates metabolism
Keywords keywords;AF-2 helix, ligand binding pocket, three-layer helical sandwich, TRANSCRIPTION REGULATOR FXR, BAR, NR1H4, bile acid receptor, NHR, nuclear receptor, corepressor, Transcription, Transcription regulation ;; 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.

4wvd__assembly_1__model_1

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

Download this curve (.dat)

4wvd__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.

4wvd__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）19.13 Å
Rg (electron density)17.81 Å
Total Rg18.79 Å
Atom count1842
Residues226
Excluded volume32966 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4wvd__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4wvd__assembly_2__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 (5)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4wvdA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id4wvdB00
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 (1)