6VGH

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
R-Value Work: 0.216
R-Value Observed: 0.218

Starting Model: experimental
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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
Modelled 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.274
R-Value Work: 0.216
R-Value Observed: 0.218
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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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.