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- PDB-2hda: Yes SH3 domain -

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Basic information

Entry
Database: PDB / ID: 2hda
TitleYes SH3 domain
ComponentsProto-oncogene tyrosine-protein kinase Yes
KeywordsTRANSFERASE / main beta
Function / homology
Function and homology information


regulation of D-glucose transmembrane transport / regulation of vascular permeability / Co-stimulation by CD28 / EPH-Ephrin signaling / Regulation of KIT signaling / leukocyte migration / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis ...regulation of D-glucose transmembrane transport / regulation of vascular permeability / Co-stimulation by CD28 / EPH-Ephrin signaling / Regulation of KIT signaling / leukocyte migration / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / PECAM1 interactions / FCGR activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / T cell costimulation / cellular response to retinoic acid / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / phosphotyrosine residue binding / EPHB-mediated forward signaling / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / actin filament / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / Signaling by SCF-KIT / protein modification process / Signaling by CSF1 (M-CSF) in myeloid cells / protein tyrosine kinase activity / transmembrane transporter binding / cell differentiation / signaling receptor binding / focal adhesion / centrosome / enzyme binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / ATP binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase Yes, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains ...Tyrosine-protein kinase Yes, SH3 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Yes
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCamara-Artigas, A. / Luque, I. / Ruiz-Sanz, J. / Mateo, P.L. / Martin-Garcia, J.M.
CitationJournal: Febs Lett. / Year: 2007
Title: Crystallographic structure of the SH3 domain of the human c-Yes tyrosine kinase: Loop flexibility and amyloid aggregation.
Authors: Martin-Garcia, J.M. / Luque, I. / Mateo, P.L. / Ruiz-Sanz, J. / Camara-Artigas, A.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Yes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2252
Polymers7,1291
Non-polymers961
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Proto-oncogene tyrosine-protein kinase Yes
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)43,34912
Polymers42,7736
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area8530 Å2
ΔGint-162 kcal/mol
Surface area16400 Å2
MethodPISA
3
A: Proto-oncogene tyrosine-protein kinase Yes
hetero molecules

A: Proto-oncogene tyrosine-protein kinase Yes
hetero molecules

A: Proto-oncogene tyrosine-protein kinase Yes
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6756
Polymers21,3863
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.009, 46.009, 90.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-51-

SO4

21A-51-

SO4

31A-34-

HOH

41A-38-

HOH

51A-39-

HOH

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Components

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


Mass: 7128.813 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YES1, YES / Production host: Escherichia coli (E. coli)
References: UniProt: P07947, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6 M ammonium sulphate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 15K, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jan 30, 2006 / Details: Montel optics
RadiationMonochromator: Bruker Microfocus (Montel Optics) Microstar / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 5626 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.08 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.0469 / Rsym value: 0.025 / Net I/σ(I): 28.37
Reflection shellResolution: 1.81→1.95 Å / Redundancy: 4.19 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 5.19 / Num. unique all: 1058 / Rsym value: 0.1825 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FYN

1fyn


Resolution: 1.9→14.86 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU B: 2.452 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.186 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26969 218 4.5 %RANDOM
Rwork0.21391 ---
all0.22 4663 --
obs0.21619 4655 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms473 0 5 41 519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022485
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.928660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.733558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10423.7524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8261572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.228153
X-RAY DIFFRACTIONr_chiral_restr0.1480.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02376
X-RAY DIFFRACTIONr_nbd_refined0.2280.2183
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2329
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2510.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.28
X-RAY DIFFRACTIONr_mcbond_it2.9712293
X-RAY DIFFRACTIONr_mcangle_it4.1693466
X-RAY DIFFRACTIONr_scbond_it3.8362223
X-RAY DIFFRACTIONr_scangle_it5.2353194
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 17 -
Rwork0.203 325 -
obs--100 %

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