5WGQ

Estrogen Receptor Alpha Ligand Binding Domain in Complex with Estradiol and SRC2-BCP1

PDB DOI: https://doi.org/10.2210/pdb5WGQ/pdb

Classification: transcription/transcription inhibitor
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-07-14 Released: 2018-06-13
Deposition Author(s): Fanning, S.W., Speltz, T.E., Mayne, C.G., Siddiqui, Z., Greene, G.L., Tajkhorshid, E., Moore, T.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free: 0.257
R-Value Work: 0.199
R-Value Observed: 0.202

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

A "cross-stitched" peptide with improved helicity and proteolytic stability.

Speltz, T.E., Mayne, C.G., Fanning, S.W., Siddiqui, Z., Tajkhorshid, E., Greene, G.L., Moore, T.W.

(2018) Org Biomol Chem 16: 3702-3706

PubMed: 29725689 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/c8ob00790j
Primary Citation of Related Structures:
5WGD, 5WGQ

PubMed Abstract:
A new computational approach to obtain quantitative energy profiles for helix folding was used in the design of orthogonal hydrocarbon and lactam bicyclic peptides. The proteolytically stable, "cross-stitched" peptide SRC2-BCP1 shows nanomolar affinity for estrogen receptor α and X-ray crystallography confirms a helical binding pose.

Organizational Affiliation

Department of Medicinal Chemistry and Pharmacognosy and UI Cancer Center, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA. twmoore@uic.edu.

Macromolecule Content

Total Structure Weight: 62.87 kDa
Atom Count: 3,866
Modelled Residue Count: 484
Deposited Residue Count: 548
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	A, B	261	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SRC2-BCP1	C [auth E], D [auth F]	13	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596 Go to UniProtKB: Q15596
PHAROS: Q15596 GTEx: ENSG00000140396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15596
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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8 Query on MK8	C [auth E], D [auth F]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002318 Query on PRD_002318	C [auth E], D [auth F]	SRC2-BCP1	Oligopeptide / Inhibitor		Interactions Focus chain C [auth E] Focus chain D [auth F] Interactions & Density Focus chain C [auth E] Focus chain D [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free: 0.257
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 54.038	α = 90
b = 84.044	β = 111.25
c = 58.209	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-06-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-06-13
Type: Initial release
Version 1.1: 2018-07-25
Changes: Data collection, Structure summary
Version 1.2: 2020-02-26
Changes: Advisory, Derived calculations
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-10-30
Changes: Structure summary