4ZI1 | pdb_00004zi1

HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH KB095285 AND CIA12 COACTIVATOR PEPTIDE

PDB DOI: https://doi.org/10.2210/pdb4ZI1/pdb

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

Deposited: 2015-04-27 Released: 2016-06-29
Deposition Author(s): Kauppi, B., Bonn, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.223 (Depositor), 0.238 (DCC)
R-Value Work:
0.175 (Depositor), 0.209 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH KB095285 AND CIA12 COACTIVATOR PEPTIDE

Kauppi, B., Bonn, T.

To be published.

Macromolecule Content

Total Structure Weight: 29.63 kDa
Atom Count: 2,122
Modeled Residue Count: 238
Deposited Residue Count: 261
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A	249	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92731
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 5	B	12	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCD5 (Homo sapiens) Explore Q9HCD5 Go to UniProtKB: Q9HCD5
PHAROS: Q9HCD5 GTEx: ENSG00000124160
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HCD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KB0 Query on KB0 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-(4-hydroxyphenyl)-7-methyl-3-phenyl-1H-inden-5-ol C₂₂ H₁₈ O₂ KXVQYSIZQKFFIZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223 (Depositor), 0.238 (DCC)
R-Value Work: 0.175 (Depositor), 0.209 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.258	α = 90
b = 85.258	β = 90
c = 112.14	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
TRUNCATE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.