6VGH | pdb_00006vgh

Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant In Complex with Lasofoxifene

PDB DOI: https://doi.org/10.2210/pdb6VGH/pdb

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

Deposited: 2020-01-08 Released: 2020-02-12
Deposition Author(s): Fanning, S.W., Greene, G.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.274 (Depositor), 0.275 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Ligand Binding Domain

Fanning, S.W.

To be published.

Macromolecule Content

Total Structure Weight: 60.9 kDa
Atom Count: 3,925
Modeled Residue Count: 456
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	262	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03372
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C3D (Subject of Investigation/LOI) Query on C3D Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	(5R,6S)-6-PHENYL-5-[4-(2-PYRROLIDIN-1-YLETHOXY)PHENYL]-5,6,7,8-TETRAHYDRONAPHTHALEN-2-OL C₂₈ H₃₁ N O₂ GXESHMAMLJKROZ-IAPPQJPRSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.274 (Depositor), 0.275 (DCC)
R-Value Work: 0.216 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.692	α = 90
b = 58.692	β = 90
c = 276.475	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-02-12
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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.