7R62 | pdb_00007r62

Estrogen Receptor Alpha Ligand Binding Domain in Complex with a Desmethyl ICI164,384 Derivative

PDB DOI: https://doi.org/10.2210/pdb7R62/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-22 Released: 2022-07-06
Deposition Author(s): Diennet, M., El Ezzy, M., Thiombane, K., Cotnoir-White, D., Poupart, J., Gao, Z., Mendoza Sanchez, R., Marinier, A., Gleason, J., Greene, G.L., Mader, S.C., Fanning, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.230 (Depositor), 0.236 (DCC)
R-Value Work:
0.201 (Depositor), 0.205 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Estrogen Receptor Alpha Ligand Binding Domain in Complex with a Desmethyl ICI164,384 Derivative

Fanning, S.W.

To be published.

Macromolecule Content

Total Structure Weight: 28.87 kDa
Atom Count: 2,270
Modeled Residue Count: 234
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	249	Homo sapiens	Mutation(s): 0 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03372
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3YJ (Subject of Investigation/LOI) Query on 3YJ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	11-[3,17beta-dihydroxyestra-1,3,5(10)-trien-7beta-yl]-N-methyl-N-propylundecanamide C₃₃ H₅₃ N O₃ UUJHTDRJNXJHMK-XEXYCPDTSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.230 (Depositor), 0.236 (DCC)
R-Value Work: 0.201 (Depositor), 0.205 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.709	α = 90
b = 58.709	β = 90
c = 274.292	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Cotnoir-White, D.

Mendoza Sanchez, R.

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, 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.