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- PDB-4xz0: ZAP-70-tSH2:compound-A complex -

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Basic information

Entry
Database: PDB / ID: 4xz0
TitleZAP-70-tSH2:compound-A complex
ComponentsTyrosine-protein kinase ZAP-70
KeywordsTransferase/Transferase inhibitor / Tyrosine kinase / cysteine adduct / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


T cell aggregation / T cell migration / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / beta selection / positive thymic T cell selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / T cell receptor complex / B cell activation ...T cell aggregation / T cell migration / positive regulation of alpha-beta T cell proliferation / negative thymic T cell selection / beta selection / positive thymic T cell selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / T cell receptor complex / B cell activation / Translocation of ZAP-70 to Immunological synapse / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / positive regulation of calcium-mediated signaling / extrinsic component of cytoplasmic side of plasma membrane / phosphotyrosine residue binding / T cell activation / calcium-mediated signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / cell-cell junction / T cell receptor signaling pathway / protein tyrosine kinase activity / adaptive immune response / cell differentiation / intracellular signal transduction / immune response / protein phosphorylation / signaling receptor binding / innate immune response / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Syk Kinase; Chain A, domain 2 / Syk Kinase; Chain A, domain 2 / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4N5 / Tyrosine-protein kinase ZAP-70
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBarros, T. / Kuriyan, J. / Visperas, P.R. / Winger, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)1RC2-AR058947-01 United States
CitationJournal: Biochem. J. / Year: 2015
Title: Modification by covalent reaction or oxidation of cysteine residues in the tandem-SH2 domains of ZAP-70 and Syk can block phosphopeptide binding.
Authors: Visperas, P.R. / Winger, J.A. / Horton, T.M. / Shah, N.H. / Aum, D.J. / Tao, A. / Barros, T. / Yan, Q. / Wilson, C.G. / Arkin, M.R. / Weiss, A. / Kuriyan, J.
History
DepositionFeb 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase ZAP-70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1014
Polymers29,5321
Non-polymers5693
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-33 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.418, 103.418, 52.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Tyrosine-protein kinase ZAP-70 / 70 kDa zeta-chain associated protein / Syk-related tyrosine kinase


Mass: 29531.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAP70, SRK / Production host: Escherichia coli (E. coli)
References: UniProt: P43403, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-4N5 / 1-(3-{5-[(3-chlorobenzyl)sulfonyl]-1H-tetrazol-1-yl}phenyl)ethanone


Mass: 376.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13ClN4O3S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsStarting compound A (4N5):1-(3-{5-[(3-chlorobenzyl)sulfonyl]-1H-tetrazol-1-yl}phenyl)ethanone, atom ...Starting compound A (4N5):1-(3-{5-[(3-chlorobenzyl)sulfonyl]-1H-tetrazol-1-yl}phenyl)ethanone, atom CAF of 4N5 A 301 covalently linked to SG atom of CYS A 117 in this structure.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, ammonium sulfate, TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.5 Å / Num. obs: 21977 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
Aimlessdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OQ1

2oq1


Resolution: 2→25.854 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 1083 4.94 %
Rwork0.2124 --
obs0.214 21942 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→25.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 24 78 2155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042131
X-RAY DIFFRACTIONf_angle_d0.8562886
X-RAY DIFFRACTIONf_dihedral_angle_d13.813801
X-RAY DIFFRACTIONf_chiral_restr0.03299
X-RAY DIFFRACTIONf_plane_restr0.003374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.09110.36061550.31212560X-RAY DIFFRACTION100
2.0911-2.20130.29331090.27432641X-RAY DIFFRACTION100
2.2013-2.33910.28561400.26022557X-RAY DIFFRACTION100
2.3391-2.51960.27851370.25992603X-RAY DIFFRACTION100
2.5196-2.77290.30331330.24232606X-RAY DIFFRACTION100
2.7729-3.17350.27451510.23952566X-RAY DIFFRACTION100
3.1735-3.99590.24471280.20282653X-RAY DIFFRACTION100
3.9959-25.85660.1961300.17492673X-RAY DIFFRACTION100

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