5JMM | pdb_00005jmm

Crystal structure of hERa-LBD (Y537S) in complex with biochanin A

PDB DOI: https://doi.org/10.2210/pdb5JMM/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3), synthetic construct
Mutation(s): Yes

Deposited: 2016-04-29 Released: 2017-05-10
Deposition Author(s): Delfosse, V., Bourguet, W.
Funding Organization(s): ANSES

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.216 (Depositor), 0.218 (DCC)
R-Value Work:
0.165 (Depositor), 0.169 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of hERa-LBD (Y537S) in complex with biochanin A

Delfosse, V., Bourguet, V.

To be published.

Macromolecule Content

Total Structure Weight: 62.12 kDa
Atom Count: 4,110
Modeled Residue Count: 485
Deposited Residue Count: 536
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A	255	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03372
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	B	255	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03372
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	C [auth F], D [auth G]	13	Homo sapiens	Mutation(s): 0 Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788 Go to UniProtKB: Q15788
PHAROS: Q15788 GTEx: ENSG00000084676
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QSO Query on QSO 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]	5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one C₁₆ H₁₂ O₅ WUADCCWRTIWANL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B]	G [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain I [auth B] Interactions & Density Focus chain G [auth B] Focus chain I [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.216 (Depositor), 0.218 (DCC)
R-Value Work: 0.165 (Depositor), 0.169 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.4	α = 90
b = 81.22	β = 109.76
c = 58.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Delfosse, V.

Bourguet, W.

Funding Organization	Location	Grant Number
ANSES	France	EST-2013/1/031

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary