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- PDB-5mtj: Yes1-SH2 in complex with monobody Mb(Yes_1) -

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Basic information

Entry
Database: PDB / ID: 5mtj
TitleYes1-SH2 in complex with monobody Mb(Yes_1)
Components
  • Monobody Mb(Yes_1)
  • Tyrosine-protein kinase Yes
KeywordsSIGNALING PROTEIN / Monobody / Src homology / Signaling
Function / homology
Function and homology information


PECAM1 interactions / Signaling by ERBB2 / Co-stimulation by CD28 / Regulation of KIT signaling / EPHA-mediated growth cone collapse / Co-inhibition by CTLA4 / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / Signaling by SCF-KIT / FCGR activation ...PECAM1 interactions / Signaling by ERBB2 / Co-stimulation by CD28 / Regulation of KIT signaling / EPHA-mediated growth cone collapse / Co-inhibition by CTLA4 / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / Signaling by SCF-KIT / FCGR activation / regulation of D-glucose transmembrane transport / Regulation of signaling by CBL / anchoring junction / cellular response to transforming growth factor beta stimulus / cellular response to retinoic acid / cellular response to platelet-derived growth factor stimulus / phosphotyrosine residue binding / actin filament / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / transmembrane transporter binding / centrosome / enzyme binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase Yes, SH3 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains ...Tyrosine-protein kinase Yes, SH3 domain / SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Yes
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsSha, F. / Kukenshoner, T. / Koide, S. / Hantschel, O.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies.
Authors: Kukenshoner, T. / Schmit, N.E. / Bouda, E. / Sha, F. / Pojer, F. / Koide, A. / Seeliger, M. / Koide, S. / Hantschel, O.
History
DepositionJan 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 2.0Aug 14, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy / _reflns_shell.pdbx_Rrim_I_all
Revision 2.1Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 2.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Tyrosine-protein kinase Yes
B: Monobody Mb(Yes_1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5685
Polymers24,0302
Non-polymers5393
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-14 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.864, 101.864, 139.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-267-

HOH

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Components

#1: Protein Tyrosine-protein kinase Yes / Proto-oncogene c-Yes / p61-Yes


Mass: 13295.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Yes1, Yes
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04736, non-specific protein-tyrosine kinase
#2: Protein Monobody Mb(Yes_1)


Mass: 10733.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: synthetic / Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.77 Å3/Da / Density % sol: 67.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.25
Details: 2M Ammonium sulfate, 0.2M Lithium sulfate, 0.1M CAPS/NaOH pH10.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.949→50 Å / Num. obs: 27106 / % possible obs: 99.82 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.04 / Rrim(I) all: 0.131 / Net I/σ(I): 24.44
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 1.5 / Rpim(I) all: 0.544 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2M and 4TZI

3k2m

4tzi


Resolution: 1.949→43.308 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.51
RfactorNum. reflection% reflection
Rfree0.2231 1361 5.02 %
Rwork0.1902 --
obs0.1918 27104 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.949→43.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 33 240 1913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081729
X-RAY DIFFRACTIONf_angle_d0.8722356
X-RAY DIFFRACTIONf_dihedral_angle_d12.7511019
X-RAY DIFFRACTIONf_chiral_restr0.057256
X-RAY DIFFRACTIONf_plane_restr0.006293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9492-2.01890.2861280.27752521X-RAY DIFFRACTION99
2.0189-2.09970.24831520.232515X-RAY DIFFRACTION100
2.0997-2.19520.22781330.22152531X-RAY DIFFRACTION100
2.1952-2.3110.25541400.21062532X-RAY DIFFRACTION100
2.311-2.45570.24691320.21022548X-RAY DIFFRACTION100
2.4557-2.64530.25771380.21212558X-RAY DIFFRACTION100
2.6453-2.91150.23981320.20552586X-RAY DIFFRACTION100
2.9115-3.33270.24171370.1842582X-RAY DIFFRACTION100
3.3327-4.19820.19411330.15842615X-RAY DIFFRACTION100
4.1982-43.31860.19051360.17462755X-RAY DIFFRACTION100

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