5WGD

Estrogen Receptor Alpha Ligand Binding Domain in Complex with Estradiol and SRC2-LP1

• PDB DOI: https://doi.org/10.2210/pdb5WGD/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-07-14 Released: 2018-06-13 
• Deposition Author(s): Fanning, S.W., Speltz, T.E., Mayne, C.G., Siddiqui, Z., Greene, G.L., Tajkhorshid, E., Moore, T.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.208 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

A "cross-stitched" peptide with improved helicity and proteolytic stability.

Speltz, T.E., Mayne, C.G., Fanning, S.W., Siddiqui, Z., Tajkhorshid, E., Greene, G.L., Moore, T.W.

(2018) Org Biomol Chem 16: 3702-3706

• PubMed: 29725689 
• DOI: https://doi.org/10.1039/c8ob00790j
• Primary Citation of Related Structures:  
  5WGD, 5WGQ


• PubMed Abstract: 
  

  A new computational approach to obtain quantitative energy profiles for helix folding was used in the design of orthogonal hydrocarbon and lactam bicyclic peptides. The proteolytically stable, "cross-stitched" peptide SRC2-BCP1 shows nanomolar affinity for estrogen receptor α and X-ray crystallography confirms a helical binding pose.

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Organizational Affiliation: 

Department of Medicinal Chemistry and Pharmacognosy and UI Cancer Center, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 62.62 kDa 
• Atom Count: 4,184 
• Modelled Residue Count: 475 
• Deposited Residue Count: 547 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	261	Homo sapiens	Mutation(s): 1  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(ACE)HKILHKLLQDS(NH2)	C [auth E]	13	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
(ACE)AILHKLLQDS(NH2)	D [auth F]	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EST	E [auth A], F [auth B]	ESTRADIOL C18 H24 O2 VOXZDWNPVJITMN-ZBRFXRBCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EST	BindingDB:  5WGD	Ki: min: 0.11, max: 100 (nM) from 14 assay(s)
		Kd: min: 0.2, max: 3.5 (nM) from 3 assay(s)
		IC50: min: 1.00e-2, max: 46 (nM) from 50 assay(s)
		EC50: min: 4.00e-3, max: 10 (nM) from 53 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.208 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.037	α = 90
b = 83.831	β = 108.32
c = 58.375	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Fanning, S.W., Speltz, T.E., Mayne, C.G., Siddiqui, Z., Greene, G.L., Tajkhorshid, E., Moore, T.W.

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Advisory, Derived calculations
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary