6VIF: Human LRH-1 ligand-binding domain

Human LRH-1 ligand-binding domain bound to agonist cpd 15 and fragment of coregulator TIF-2. Determined by X-ray diffraction at 2.26 Å resolution. Released 10 Jun 2020.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,047
Mol. weight: 30.52 kDa
Ligands: QY4
Released: 10 Jun 2020

Explore 6VIF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VIF contains 14 α-helices and 2 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	303-310	8
α-helix	315-331	17
α-helix	335-337	3
α-helix	338-340	3
α-helix	341-361	21
α-helix	366-368	3
α-helix	371-396	26
β-strand	402-404	3	1
β-strand	410-412	3	1
α-helix	413-420	8
α-helix	422-440	19
α-helix	445-456	12
α-helix	467-487	21
α-helix	495-522	28
α-helix	531-536	6

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	743-750	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear receptor subfamily 5 group A member 2	A	protein	245	Homo sapiens	O00482 (AlphaFold model)
Nuclear receptor coactivator 2	B	protein	14	Homo sapiens	Q15596 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VIF_1 Nuclear receptor subfamily 5 group A member 2 (chains A)
SNASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSI
VEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSII
ASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQ
VNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEML
HAKRA

Sequence of entity 2 (B), FASTA

>6VIF_2 Nuclear receptor coactivator 2 (chains B)
KENALLRYLLDKDD

Ligands and cofactors

ID	Name	Formula	Copies
QY4	N-[(8beta,11alpha,12alpha)-8-{[methyl(phenyl)amino]methyl}-1,6:7,14-dicyclopros…	C28 H39 N3 O2 S	1

Primary citation

Development of a new class of liver receptor homolog-1 (LRH-1) agonists by photoredox conjugate addition. Cornelison, J.L., Cato, M.L., Johnson, A.M. et al. Bioorg Med Chem Lett (2020) 30:127293-127293. DOI 10.1016/j.bmcl.2020.127293 · PubMed

Other PDB entries of the same protein (UniProt O00482 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6VC2 1.7 Å, LRH-1 bound to SS-RJW100 and a fragment of the Tif2 Coactivator
3PLZ 1.75 Å, Human LRH1 LBD bound to GR470
4PLD 1.75 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a…
4PLE 1.75 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to an E. Coli…
4ONI 1.8 Å, Structure of Human Orphan Receptor LRH1 bound to two bacterial phospholipids
5L11 1.85 Å, Human Liver Receptor Homologue-1 (LRH-1) Bound to RJW100 and a Fragment of TIF-2
4RWV 1.86 Å, Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1,…
1YUC 1.9 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a…
4DOR 1.9 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a…
5SYZ 1.93 Å, Human Liver Receptor Homologue-1 (LRH-1) Bound to a RJW100 stereoisomer and a Fragment…
5UNJ 1.96 Å, Structure of Human Liver Receptor Homolog 1 in complex with PGC1a and RJW100
4DOS 2.0 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to DLPC and a Fragment…

Browse structure collections

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