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- PDB-7f8h: Structure-activity relationship studies of allosteric inhibitors ... -

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Basic information

Entry
Database: PDB / ID: 7f8h
TitleStructure-activity relationship studies of allosteric inhibitors of EYA2 tyrosine phosphatase
ComponentsEyes absent homolog 2
KeywordsTRANSCRIPTION / eya2 / eyes absent protein / phosphatase / transcription coactivator
Function / homology
Function and homology information


histone H2AXY142 phosphatase activity / mesodermal cell fate specification / striated muscle tissue development / mitochondrial outer membrane permeabilization / anatomical structure development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...histone H2AXY142 phosphatase activity / mesodermal cell fate specification / striated muscle tissue development / mitochondrial outer membrane permeabilization / anatomical structure development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of DNA repair / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell differentiation / DNA repair / magnesium ion binding / mitochondrion / nucleoplasm / nucleus / cytosol
Similarity search - Function
EYA domain / Eyes absent family / EYA domain superfamily / EYA domain, metazoan / haloacid dehalogenase-like hydrolase / HAD-like superfamily
Similarity search - Domain/homology
Chem-1SI / Eyes absent homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAnantharajan, J. / Baburajendran, N.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)OFIRG17may050, NMRC/OFIRG/0051/2017 Singapore
CitationJournal: Protein Sci. / Year: 2022
Title: Structure-activity relationship studies of allosteric inhibitors of EYA2 tyrosine phosphatase.
Authors: Anantharajan, J. / Baburajendran, N. / Lin, G. / Loh, Y.Y. / Xu, W. / Ahmad, N.H.B. / Liu, S. / Jansson, A.E. / Kuan, J.W.L. / Ng, E.Y. / Yeo, Y.K. / Hung, A.W. / Joy, J. / Hill, J. / Ford, ...Authors: Anantharajan, J. / Baburajendran, N. / Lin, G. / Loh, Y.Y. / Xu, W. / Ahmad, N.H.B. / Liu, S. / Jansson, A.E. / Kuan, J.W.L. / Ng, E.Y. / Yeo, Y.K. / Hung, A.W. / Joy, J. / Hill, J. / Ford, H.L. / Zhao, R. / Keller, T.H. / Kang, C.
History
DepositionJul 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Eyes absent homolog 2
A: Eyes absent homolog 2
C: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1036
Polymers99,0793
Non-polymers1,0243
Water0
1
B: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3682
Polymers33,0261
Non-polymers3411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3682
Polymers33,0261
Non-polymers3411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3682
Polymers33,0261
Non-polymers3411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.281, 50.420, 144.281
Angle α, β, γ (deg.)90.000, 101.850, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 265 through 269 and (name N...
21(chain B and ((resid 265 through 269 and (name N...
31(chain C and (resid 265 through 309 or (resid 310...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNARGARG(chain A and ((resid 265 through 269 and (name N...AB265 - 26921 - 25
12ASNASNLEULEU(chain A and ((resid 265 through 269 and (name N...AB265 - 53821 - 294
13ASNASNLEULEU(chain A and ((resid 265 through 269 and (name N...AB265 - 53821 - 294
14ASNASNLEULEU(chain A and ((resid 265 through 269 and (name N...AB265 - 53821 - 294
15ASNASNLEULEU(chain A and ((resid 265 through 269 and (name N...AB265 - 53821 - 294
21ASNASNARGARG(chain B and ((resid 265 through 269 and (name N...BA265 - 26921 - 25
22ASNASNLEULEU(chain B and ((resid 265 through 269 and (name N...BA265 - 53821 - 294
23ASNASNLEULEU(chain B and ((resid 265 through 269 and (name N...BA265 - 53821 - 294
24ASNASNLEULEU(chain B and ((resid 265 through 269 and (name N...BA265 - 53821 - 294
25ASNASNLEULEU(chain B and ((resid 265 through 269 and (name N...BA265 - 53821 - 294
31ASNASNGLUGLU(chain C and (resid 265 through 309 or (resid 310...CC265 - 30921 - 65
32GLUGLUGLUGLU(chain C and (resid 265 through 309 or (resid 310...CC31066
33ALAALALEULEU(chain C and (resid 265 through 309 or (resid 310...CC262 - 53818 - 294
34ALAALALEULEU(chain C and (resid 265 through 309 or (resid 310...CC262 - 53818 - 294
35ALAALALEULEU(chain C and (resid 265 through 309 or (resid 310...CC262 - 53818 - 294
36ALAALALEULEU(chain C and (resid 265 through 309 or (resid 310...CC262 - 53818 - 294

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Components

#1: Protein Eyes absent homolog 2 /


Mass: 33026.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EYA2, EAB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00167, protein-tyrosine-phosphatase
#2: Chemical ChemComp-1SI / 3-fluoranyl-~{N}-[(~{E})-(5-pyridin-2-ylsulfanylfuran-2-yl)methylideneamino]benzamide


Mass: 341.359 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H12FN3O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium citrate tribasic dihydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 3.2→91.01 Å / Num. obs: 17269 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 98.39 Å2 / CC1/2: 0.989 / Net I/σ(I): 6.8
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 3.8 % / Num. unique obs: 3080 / CC1/2: 0.842 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZMA

5zma


Resolution: 3.3→56.003 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 1565 10.01 %
Rwork0.234 14065 -
obs0.2389 15630 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.63 Å2 / Biso mean: 101.7066 Å2 / Biso min: 49.25 Å2
Refinement stepCycle: final / Resolution: 3.3→56.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 72 0 5980
Biso mean--77.87 --
Num. residues----778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026104
X-RAY DIFFRACTIONf_angle_d0.4988299
X-RAY DIFFRACTIONf_chiral_restr0.041963
X-RAY DIFFRACTIONf_plane_restr0.0021051
X-RAY DIFFRACTIONf_dihedral_angle_d2.2033586
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3442X-RAY DIFFRACTION5.272TORSIONAL
12B3442X-RAY DIFFRACTION5.272TORSIONAL
13C3442X-RAY DIFFRACTION5.272TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.40650.3881390.3163124499
3.4065-3.52830.3541380.3015126499
3.5283-3.66950.37471370.2882125099
3.6695-3.83650.35821450.27361287100
3.8365-4.03870.31861390.263124299
4.0387-4.29160.28891420.22721281100
4.2916-4.62290.24421440.20851287100
4.6229-5.08780.25591450.2141273100
5.0878-5.82330.30221430.24321291100
5.8233-7.33420.28241440.24691304100
7.3342-56.0030.22181490.1951134299

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