3OLS

Crystal structure of estrogen receptor beta ligand binding domain

PDB DOI: https://doi.org/10.2210/pdb3OLS/pdb

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

Deposited: 2010-08-26 Released: 2010-11-17
Deposition Author(s): Moecklinghoff, S., Rose, R., Carraz, M., Visser, A., Ottmann, C., Brunsveld, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.266
R-Value Work: 0.184
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Synthesis and crystal structure of a phosphorylated estrogen receptor ligand binding domain.

Mocklinghoff, S., Rose, R., Carraz, M., Visser, A., Ottmann, C., Brunsveld, L.

(2010) Chembiochem 11: 2251-2254

PubMed: 20922740 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201000532
Primary Citation of Related Structures:
3OLL, 3OLS

Organizational Affiliation

Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, NL.

Macromolecule Content

Total Structure Weight: 59.23 kDa
Atom Count: 4,106
Modelled Residue Count: 473
Deposited Residue Count: 518
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	240	Homo sapiens	Mutation(s): 0 Gene Names: ESR2, ESTRB, NR3A2
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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
Nuclear receptor coactivator 1	C, D	19	Homo sapiens	Mutation(s): 0 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788 Go to UniProtKB: Q15788
PHAROS: Q15788 GTEx: ENSG00000084676
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EST Query on EST 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]	ESTRADIOL C₁₈ H₂₄ O₂ VOXZDWNPVJITMN-ZBRFXRBCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
EST	BindingDB: 3OLS	Ki: min: 0.01, max: 100 (nM) from 10 assay(s)
		Kd: min: 0.5, max: 4.1 (nM) from 2 assay(s)
		IC50: min: 1.00e-2, max: 24 (nM) from 37 assay(s)
		EC50: min: 1.00e-2, max: 30 (nM) from 44 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.266
R-Value Work: 0.184
R-Value Observed: 0.188
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.43	α = 90
b = 70.43	β = 90
c = 110.53	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-11-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations