1QKM

HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN

> Summary

Summary for 1QKM

Related1ERR 1QKN
DescriptorESTROGEN RECEPTOR BETA
Functional Keywordsnuclear receptor, transcription factor, phyto-oestrogen, partial agonist
Biological sourceHOMO SAPIENS (HUMAN)
Cellular locationNucleus Q92731
Total number of polymer chains1
Total molecular weight28996.49
Authors
Pike, A.C.W.,Brzozowski, A.M.,Carlquist, M. (deposition date: 1999-07-27, release date: 2000-07-28, modification date: 2009-02-24)
Primary citation
Pike, A.C.W.,Brzozowski, A.M.,Hubbard, R.E.,Bonn, T.,Thorsell, A.-G.,Engstrom, O.,Ljunggren, J.,Gustaffson, J.-A.,Carlquist, M.
Structure of the Ligand-Binding Domain of Oestrogen Receptor Beta in the Presence of a Partial Agonist and a Full Antagonist
Embo J., 18:4608-, 1999
PubMed: 10469641
DOI: 10.1093/EMBOJ/18.17.4608
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.8 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.248802.5%6.5%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1qkm
no rotation
Molmil generated image of 1qkm
rotated about x axis by 90°
Molmil generated image of 1qkm
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1qkm
no rotation
Molmil generated image of 1qkm
rotated about x axis by 90°
Molmil generated image of 1qkm
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (1qkm.pdb1.gz [81.79 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AESTROGEN RECEPTOR BETApolymer25528726.21
UniProt (Q92731)
Pfam (PF00104)
HOMO SAPIENS (HUMAN)@PDBjOESTROGEN RECEPTOR, ER-LBD
GENISTEINnon-polymer270.21
waterwater18.0139

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight28726.2
Non-Polymers*Number of molecules1
Total molecular weight270.2
All*Total molecular weight28996.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.8 Å)

Cell axes63.12063.120250.230
Cell angles90.0090.00120.00
SpacegroupP 61 2 2
Resolution limits55.00 - 1.80
the highest resolution shell value -
R-work0.21500
R-free0.25200
RMSD bond length0.013
RMSD bond angle0.030

Data Collection Statistics

Resolution limits60.00 - 1.80
the highest resolution shell value -
Number of reflections28523
Number of measurements358818*
Rmerge_l_obs0.049*
the highest resolution shell value0.433*
Completeness99.7
the highest resolution shell value100*
Redundancy8
the highest resolution shell value8
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1Vapor diffusion, hanging drop*8.1unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein8 (mg/ml)
21reservoirPEG60006-9 (%(w/v))
31reservoir1.6-2.1 (M)
41reservoirTris-HCl0.1 (M)
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
A0005929cellular_componentcilium
A0005576cellular_componentextracellular region
A0005739cellular_componentmitochondrion
A0043005cellular_componentneuron projection
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0043204cellular_componentperikaryon
A0048471cellular_componentperinuclear region of cytoplasm
A0005886cellular_componentplasma membrane
A0032993cellular_componentprotein-DNA complex
A0001046molecular_functioncore promoter sequence-specific DNA binding
A0003677molecular_functionDNA binding
A0008144molecular_functiondrug binding
A0019899molecular_functionenzyme binding
A1903924molecular_functionestradiol binding
A0030284molecular_functionestrogen receptor activity
A0034056molecular_functionestrogen response element binding
A0048019molecular_functionreceptor antagonist activity
A0038052molecular_functionRNA polymerase II transcription factor activity, estrogen-activated sequence-specific DNA binding
A0004879molecular_functionRNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
A0005496molecular_functionsteroid binding
A1990239molecular_functionsteroid hormone binding
A0003707molecular_functionsteroid hormone receptor activity
A0003713molecular_functiontranscription coactivator activity
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0008270molecular_functionzinc ion binding
A0021764biological_processamygdala development
A0001662biological_processbehavioral fear response
A0007267biological_processcell-cell signaling
A0035690biological_processcellular response to drug
A0071392biological_processcellular response to estradiol stimulus
A0071259biological_processcellular response to magnetism
A0021549biological_processcerebellum development
A0044849biological_processestrous cycle
A0021854biological_processhypothalamus development
A0030520biological_processintracellular estrogen receptor signaling pathway
A0007611biological_processlearning or memory
A0030308biological_processnegative regulation of cell growth
A0050680biological_processnegative regulation of epithelial cell proliferation
A2000252biological_processnegative regulation of feeding behavior
A1901215biological_processnegative regulation of neuron death
A2000378biological_processnegative regulation of reactive oxygen species metabolic process
A0048662biological_processnegative regulation of smooth muscle cell proliferation
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0001541biological_processovarian follicle development
A0043065biological_processpositive regulation of apoptotic process
A0045742biological_processpositive regulation of epidermal growth factor receptor signaling pathway
A0070374biological_processpositive regulation of ERK1 and ERK2 cascade
A0051091biological_processpositive regulation of sequence-specific DNA binding transcription factor activity
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0045893biological_processpositive regulation of transcription, DNA-templated
A0045909biological_processpositive regulation of vasodilation
A0030850biological_processprostate gland development
A0043523biological_processregulation of neuron apoptotic process
A0006355biological_processregulation of transcription, DNA-templated
A0014823biological_processresponse to activity
A1903925biological_processresponse to bisphenol A
A0071548biological_processresponse to dexamethasone
A0045471biological_processresponse to ethanol
A0033595biological_processresponse to genistein
A0044752biological_processresponse to human chorionic gonadotropin
A0017085biological_processresponse to insecticide
A0031667biological_processresponse to nutrient levels
A1902074biological_processresponse to salt
A0033574biological_processresponse to testosterone
A0009414biological_processresponse to water deprivation
A0060009biological_processSertoli cell development
A0060011biological_processSertoli cell proliferation
A0007165biological_processsignal transduction
A0006367biological_processtranscription initiation from RNA polymerase II promoter
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC19BINDING SITE FOR RESIDUE GEN A 600
ChainResidue
AMET41
ALEU44
AGLU51
AMET82
ALEU85
AARG92
AILE122
AHIS221
ALEU222

?

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
GEN_1qkm_A_60019GENISTEIN binding site
ChainResidueligand
AMET295GEN: GENISTEIN
ALEU298-THR299GEN: GENISTEIN
ALEU301-ALA302GEN: GENISTEIN
AGLU305GEN: GENISTEIN
AMET336GEN: GENISTEIN
ALEU339-MET340GEN: GENISTEIN
ALEU343GEN: GENISTEIN
AARG346GEN: GENISTEIN
APHE356GEN: GENISTEIN
AILE373GEN: GENISTEIN
AILE376GEN: GENISTEIN
ALEU380GEN: GENISTEIN
AGLY472GEN: GENISTEIN
AHIS475-LEU476GEN: GENISTEIN
AMET479GEN: GENISTEIN

?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Nuclear receptor.
ChainResidueDetails
ANA*

?

Catalytic Information from CSA

site_idNumber of ResiduesDetails
?

Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan