7XWP: Estrogen receptor beta

Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-3-(2-chloro-4-hydroxyphenyl)-2-(4-hydroxyphenyl)propanenitrile. Determined by X-ray diffraction at 1.92 Å resolution. Released 20 Jul 2022.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,714
Mol. weight: 58.73 kDa
Ligands: I1I
Released: 20 Jul 2022

Explore 7XWP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XWP contains 26 α-helices and 4 β-strands across 4 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: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	265-275	11
α-helix	276-280	5
α-helix	292-314	23
α-helix	319-321	3
α-helix	324-347	24
β-strand	354-357	4	1
β-strand	360-362	3	1
α-helix	364-368	5
α-helix	373-389	17
α-helix	394-406	13
α-helix	422-443	22
α-helix	448-481	34
α-helix	489-497	9

Chain B: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	265-275	11
α-helix	276-281	6
α-helix	283-285	3
α-helix	288-289	2
α-helix	291-314	24
α-helix	319-321	3
α-helix	324-347	24
β-strand	354-357	4	2
β-strand	360-362	3	2
α-helix	364-367	4
α-helix	373-389	17
α-helix	394-406	13
α-helix	422-442	21
α-helix	448-481	34
α-helix	489-496	8

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	605-611	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Estrogen receptor beta	A, B	protein	247	Homo sapiens	Q92731 (AlphaFold model)
SRC peptide	C, D	protein	13	Homo sapiens	Q15788 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7XWP_1 Estrogen receptor beta (chains A, B)
GPLGSDALSPEQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKK
IPGFVELSLFDQVRLLESSWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKSVEGILE
IFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTD
ALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKSKNVVPVYDLLLEML
NAHVLDD

Sequence of entity 2 (C, D), FASTA

>7XWP_2 SRC peptide (chains C, D)
SGSHKLVQLLTTT

Ligands and cofactors

ID	Name	Formula	Copies
I1I	(2~{S})-3-(2-chloranyl-4-oxidanyl-phenyl)-2-(4-hydroxyphenyl)propanenitrile	C15 H12 Cl N O2	2

Primary citation

Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives. Handa, C., Yamazaki, Y., Yonekubo, S. et al. J Steroid Biochem Mol Biol (2022) 222:106152-106152. DOI 10.1016/j.jsbmb.2022.106152 · PubMed

Other PDB entries of the same protein (UniProt Q92731 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3OLL 1.5 Å, Crystal structure of phosphorylated estrogen receptor beta ligand binding domain
7XVY 1.54 Å, Human Estrogen Receptor beta Ligand-binding Domain in Complex with S-DPN
1QKM 1.8 Å, Human oestrogen receptor beta ligand-binding domain in complex with partial agonist…
7XWQ 1.89 Å, Human Estrogen Receptor beta Ligand-binding Domain in Complex with…
2YJD 1.93 Å, Stapled peptide bound to Estrogen Receptor Beta
3OMQ 1.97 Å, Fragment-Based Design of novel Estrogen Receptor Ligands
9ECF 2.0 Å, Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide…
1YYE 2.03 Å, Crystal structure of estrogen receptor beta complexed with way-202196
3OMP 2.05 Å, Fragment-Based Design of novel Estrogen Receptor Ligands
7XVZ 2.08 Å, Human Estrogen Receptor beta Ligand-binding Domain in Complex with…
2NV7 2.1 Å, Crystal Structure of Estrogen Receptor Beta Complexed with WAY-555
4J24 2.1 Å, Estrogen Receptor in complex with proline-flanked LXXLL peptides

Browse structure collections

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