2YJD: Stapled peptide

Stapled peptide bound to Estrogen Receptor Beta. Determined by X-ray diffraction at 1.93 Å resolution. Released 3 Aug 2011.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 3,960
Mol. weight: 57.47 kDa
Ligands: YJD
Released: 3 Aug 2011

Explore 2YJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YJD contains 24 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	265-274	10
α-helix	276-281	6
α-helix	291-314	24
α-helix	319-321	3
α-helix	324-347	24
β-strand	353-357	5	1
β-strand	360-363	4	1
α-helix	364-369	6
α-helix	374-389	16
α-helix	394-406	13
α-helix	423-442	20
α-helix	448-481	34
α-helix	489-496	8

Chain B: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	265-275	11
α-helix	277-281	5
α-helix	291-314	24
α-helix	324-347	24
β-strand	353-357	5	2
β-strand	360-363	4	2
α-helix	365-368	4
α-helix	373-390	18
α-helix	394-407	14
α-helix	423-442	20
α-helix	448-460	13
α-helix	462-481	20
α-helix	490-496	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Estrogen receptor beta	A, B	protein	240	HOMO SAPIENS	Q92731 (AlphaFold model)
Stapled peptide	C, D	protein	13	HOMO SAPIENS	Q15596 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2YJD_1 ESTROGEN RECEPTOR BETA (chains A, B)
DALSPEQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFV
ELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDML
LATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWV
IAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVL

Sequence of entity 2 (C, D), FASTA

>2YJD_2 STAPLED PEPTIDE (chains C, D)
XHLILHLLLQDSX

Ligands and cofactors

ID	Name	Formula	Copies
YJD	4-(2-propan-2-yloxybenzimidazol-1-yl)phenol	C16 H16 N2 O2	2

Primary citation

Design and Structure of Stapled Peptides Binding to Estrogen Receptors. Phillips, C., Roberts, L.R., Schade, M. et al. J Am Chem Soc (2011) 133:9696. DOI 10.1021/JA202946K · 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…
7XWP 1.92 Å, Human Estrogen Receptor beta Ligand-binding Domain in Complex with…
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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