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- PDB-7f8g: Structure-activity relationship studies of allosteric inhibitors ... -

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Basic information

Entry
Database: PDB / ID: 7f8g
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 / mitochondrial outer membrane permeabilization / striated muscle tissue 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 ...histone H2AXY142 phosphatase activity / mesodermal cell fate specification / mitochondrial outer membrane permeabilization / striated muscle tissue 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-1RI / Eyes absent homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.491 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,8864
Polymers66,0532
Non-polymers8332
Water00
1
B: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,0261
Non-polymers4161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Eyes absent homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,0261
Non-polymers4161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.920, 89.920, 96.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 266 through 276 or (resid 277...
21(chain B and ((resid 266 through 269 and (name N...

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
11GLUGLUASPASP(chain A and (resid 266 through 276 or (resid 277...AB266 - 27622 - 32
12GLUGLUGLUGLU(chain A and (resid 266 through 276 or (resid 277...AB27733
13GLUGLULEULEU(chain A and (resid 266 through 276 or (resid 277...AB266 - 53822 - 294
14GLUGLULEULEU(chain A and (resid 266 through 276 or (resid 277...AB266 - 53822 - 294
15GLUGLULEULEU(chain A and (resid 266 through 276 or (resid 277...AB266 - 53822 - 294
16GLUGLULEULEU(chain A and (resid 266 through 276 or (resid 277...AB266 - 53822 - 294
21GLUGLUARGARG(chain B and ((resid 266 through 269 and (name N...BA266 - 26922 - 25
22ASNASNLEULEU(chain B and ((resid 266 through 269 and (name N...BA265 - 53821 - 294
23ASNASNLEULEU(chain B and ((resid 266 through 269 and (name N...BA265 - 53821 - 294
24ASNASNLEULEU(chain B and ((resid 266 through 269 and (name N...BA265 - 53821 - 294
25ASNASNLEULEU(chain B and ((resid 266 through 269 and (name N...BA265 - 53821 - 294

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Components

#1: Protein Eyes absent homolog 2


Mass: 33026.348 Da / Num. of mol.: 2
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-1RI / 3-phenoxy-~{N}-[(~{E})-(5-pyrimidin-2-ylsulfanylfuran-2-yl)methylideneamino]benzamide


Mass: 416.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H16N4O3S / 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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02M MgCl2, 0.1M HEPES 7.5, 22% poly acrylic acid sodium salt 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9538 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 3.49→77.87 Å / Num. obs: 10772 / % possible obs: 96.7 % / Redundancy: 2 % / Biso Wilson estimate: 82.22 Å2 / CC1/2: 0.991 / Net I/σ(I): 10.7
Reflection shellResolution: 3.49→3.82 Å / Num. unique obs: 2611 / CC1/2: 0.769 / % possible all: 98

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Processing

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

5zma


Resolution: 3.491→44.96 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 1080 10.04 %
Rwork0.2135 9682 -
obs0.2191 10762 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.02 Å2 / Biso mean: 83.3167 Å2 / Biso min: 43.3 Å2
Refinement stepCycle: final / Resolution: 3.491→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 60 0 3986
Biso mean--65.46 --
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034083
X-RAY DIFFRACTIONf_angle_d0.6035555
X-RAY DIFFRACTIONf_chiral_restr0.043640
X-RAY DIFFRACTIONf_plane_restr0.003704
X-RAY DIFFRACTIONf_dihedral_angle_d2.1133216
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2218X-RAY DIFFRACTION6.914TORSIONAL
12B2218X-RAY DIFFRACTION6.914TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.491-3.64960.37211410.2862122198
3.6496-3.84190.32791340.266121798
3.8419-4.08250.28411480.2308124698
4.0825-4.39740.25611270.2206120397
4.3974-4.83950.2131410.1962121797
4.8395-5.53870.31491390.2202119396
5.5387-6.9740.28741270.2296119094
6.974-44.960.20841230.1596119595

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