Macromolecule Content

Total Structure Weight: 112.96 kDa
Atom Count: 7,207
Modelled Residue Count: 918
Deposited Residue Count: 972
Unique protein chains: 1

4XI3

Estrogen Receptor Alpha Ligand Binding Domain in Complex with Bazedoxifene

PDB DOI: 10.2210/pdb4XI3/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-01-06 Released: 2016-01-13
Deposition Author(s): Fanning, S.W., Mayne, C.G., Toy, W., Carlson, K., Greene, B., Nowak, J., Walter, R., Panchamukhi, S., Tajhorshid, E., Nettles, K.W., Chandarlapaty, S., Katzenellenbogen, J., Greene, G.L.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.268
R-Value Work: 0.215
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biochemical and Structural Basis for Constitutive Activity and Reduced SERM Potency in Acquired SERM/AI Resistant Metastatic Breast Cancers via ESR1 Somatic Mutation

Fanning, S.W., Mayne, C.G., Toy, W., Carlson, K., Greene, B., Nowak, J., Walter, R., Panchamukhi, S., Tajhorshid, E., Nettles, K.W., Chandarlapaty, S., Katzenellenbogen, J., Greene, G.L.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B, C, D	243	Homo sapiens	Mutation(s): 2 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03372
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
29S Query on 29S Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	Bazedoxifene C₃₀ H₃₄ N₂ O₃ UCJGJABZCDBEDK-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
29S	BindingDB: 4XI3	IC50: min: 0.6, max: 50 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.268
R-Value Work: 0.215
R-Value Observed: 0.218
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.575	α = 86.76
b = 59.165	β = 75.36
c = 94.144	γ = 63.03

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	BC131458P1

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2019-04-10
Changes: Author supporting evidence, Data collection, Derived calculations, Structure summary
Version 1.2: 2019-11-27
Changes: Author supporting evidence