2YJD | pdb_00002yjd

Stapled peptide bound to Estrogen Receptor Beta

PDB DOI: https://doi.org/10.2210/pdb2YJD/pdb

Classification: HORMONE RECEPTOR/PEPTIDE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-19 Released: 2011-08-03
Deposition Author(s): Phillips, C., Roberts, L.R., Schade, M., Bent, A., Davies, N.L., Moore, R., Pannifer, A.D., Brown, D.G., Pickford, A.R., Irving, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.260 (Depositor), 0.215 (DCC)
R-Value Work:
0.225 (Depositor)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Design and Structure of Stapled Peptides Binding to Estrogen Receptors.

Phillips, C., Roberts, L.R., Schade, M., Bazin, R., Bent, A., Davies, N.L., Moore, R., Pannifer, A.D., Pickford, A.R., Prior, S.H., Read, C.M., Scott, A., Brown, D.G., Xu, B., Irving, S.L.

(2011) J Am Chem Soc 133: 9696

PubMed: 21612236 Search on PubMed
DOI: https://doi.org/10.1021/ja202946k
Primary Citation Related Structures:
2LDA, 2LDC, 2LDD, 2YJA, 2YJD

PubMed Abstract:
Synthetic peptides that specifically bind nuclear hormone receptors offer an alternative approach to small molecules for the modulation of receptor signaling and subsequent gene expression. Here we describe the design of a series of novel stapled peptides that bind the coactivator peptide site of estrogen receptors. Using a number of biophysical techniques, including crystal structure analysis of receptor-stapled peptide complexes, we describe in detail the molecular interactions and demonstrate that all-hydrocarbon staples modulate molecular recognition events. The findings have implications for the design of stapled peptides in general.

Organizational Affiliation

Department of Chemistry, Pfizer, Sandwich CT13 9NJ, UK. Chris.Phillips@famco.co.uk

Macromolecule Content

Total Structure Weight: 57.47 kDa
Atom Count: 3,960
Modeled Residue Count: 472
Deposited Residue Count: 506
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR BETA	A, B	240	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731 Go to UniProtKB: Q92731
PHAROS: Q92731 GTEx: ENSG00000140009
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92731
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
STAPLED PEPTIDE	C, D	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596 Go to UniProtKB: Q15596
PHAROS: Q15596 GTEx: ENSG00000140396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15596
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YJD Query on YJD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	4-(2-PROPAN-2-YLOXYBENZIMIDAZOL-1-YL)PHENOL C₁₆ H₁₆ N₂ O₂ IRWOSCQWORJIQP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8 Query on MK8	C, D	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.260 (Depositor), 0.215 (DCC)
R-Value Work: 0.225 (Depositor)
R-Value Observed: 0.226 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.62	α = 90
b = 102.62	β = 90
c = 102.62	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2017-01-25
Changes: Atomic model, Other
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Other, Structure summary