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- PDB-1u59: Crystal Structure of the ZAP-70 Kinase Domain in Complex with Sta... -

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Basic information

Entry
Database: PDB / ID: 1u59
TitleCrystal Structure of the ZAP-70 Kinase Domain in Complex with Staurosporine
ComponentsTyrosine-protein kinase ZAP-70
KeywordsTRANSFERASE
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 / positive thymic T cell selection / beta 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 / positive thymic T cell selection / beta 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 / signaling receptor binding / protein phosphorylation / innate immune response / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / 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 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 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
STAUROSPORINE / Tyrosine-protein kinase ZAP-70
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJin, L. / Pluskey, S. / Petrella, E.C. / Cantin, S.M. / Gorga, J.C. / Rynkiewicz, M.J. / Pandey, P. / Strickler, J.E. / Babine, R.E. / Weaver, D.T. / Seidl, K.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Three-dimensional Structure of the ZAP-70 Kinase Domain in Complex with Staurosporine: IMPLICATIONS FOR THE DESIGN OF SELECTIVE INHIBITORS
Authors: Jin, L. / Pluskey, S. / Petrella, E.C. / Cantin, S.M. / Gorga, J.C. / Rynkiewicz, M.J. / Pandey, P. / Strickler, J.E. / Babine, R.E. / Weaver, D.T. / Seidl, K.J.
History
DepositionJul 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,7142
Polymers33,2481
Non-polymers4671
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.056, 57.064, 125.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33247.602 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZAP70, SRK / Plasmid: pTriEx and BacVector / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF+ / References: UniProt: P43403, EC: 2.7.1.112
#2: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, DL-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 23, 2003 / Details: Blue Osmic Mirrors
RadiationMonochromator: Blue Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 14335 / Num. obs: 14304 / % possible obs: 99.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 26.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1400 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2002refinement
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1MQB

1mqb


Resolution: 2.3→29.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 498101.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1400 10.2 %RANDOM
Rwork0.217 ---
all-14312 --
obs-13783 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1812 Å2 / ksol: 0.359298 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1-29.02 Å20 Å20 Å2
2---12.9 Å20 Å2
3----16.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 35 54 2376
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.351 140 11 %
Rwork0.322 1138 -
obs-1278 91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4STO.PARAMSTO.TOP

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