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- PDB-4two: Human EphA3 Kinase domain in complex with compound 164 -

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Basic information

Entry
Database: PDB / ID: 4two
TitleHuman EphA3 Kinase domain in complex with compound 164
ComponentsEphrin type-A receptor 3
KeywordsTRANSFERASE / TRANSFERASE/TRANSFERASE INHIBITOR
Function / homology
Function and homology information


fasciculation of sensory neuron axon / fasciculation of motor neuron axon / ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / transmembrane-ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity ...fasciculation of sensory neuron axon / fasciculation of motor neuron axon / ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / transmembrane-ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to retinoic acid / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / axon guidance / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / cell migration / actin cytoskeleton / nuclear membrane / early endosome / cell adhesion / dendrite / extracellular region / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-A receptor 3, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. ...Ephrin type-A receptor 3, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III 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. / Immunoglobulin-like fold / 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-37W / Ephrin type-A receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.047 Å
AuthorsDong, J. / Caflisch, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases.
Authors: Dong, J. / Zhao, H. / Zhou, T. / Spiliotopoulos, D. / Rajendran, C. / Li, X.D. / Huang, D. / Caflisch, A.
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Ephrin type-A receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8332
Polymers40,4581
Non-polymers3741
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.221, 38.068, 75.310
Angle α, β, γ (deg.)90.00, 100.83, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein Ephrin type-A receptor 3 / EPH-like kinase 4 / hEK4 / HEK / Human embryo kinase / Tyrosine-protein kinase TYRO4 / Tyrosine- ...EPH-like kinase 4 / hEK4 / HEK / Human embryo kinase / Tyrosine-protein kinase TYRO4 / Tyrosine-protein kinase receptor ETK1 / Eph-like tyrosine kinase 1


Mass: 40458.180 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 609-947)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA3, ETK, ETK1, HEK, TYRO4 / Plasmid: p28-LIC-Thrombin / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P29320, receptor protein-tyrosine kinase
#2: Chemical ChemComp-37W / 5-{[3-carbamoyl-4-(3,4-dimethylphenyl)-5-methylthiophen-2-yl]amino}-5-oxopentanoic acid


Mass: 374.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 0.15M ammonium sulfate, 22.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.05→38.07 Å / Num. all: 18078 / Num. obs: 18078 / % possible obs: 95.5 % / Redundancy: 2.7 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.043 / Rsym value: 0.035 / Net I/av σ(I): 20.017 / Net I/σ(I): 23 / Num. measured all: 49627
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.162.70.1378.1673224620.0990.1378.190.9
2.16-2.292.80.1117.1687224720.080.1119.794.8
2.29-2.452.80.0879646623230.0630.08712.695.4
2.45-2.642.80.0711.2610521850.0510.0714.895.9
2.64-2.892.80.04915.9563820310.0360.04919.696.3
2.89-3.242.80.03223.6507918370.0240.03227.597
3.24-3.742.70.02231.5446516380.0160.0223997.4
3.74-4.582.70.01835.8375614020.0130.01848.597.4
4.58-6.472.70.01739.7295711150.0130.01749.198.4
6.47-38.0682.50.01638.915576130.0130.01655.194.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.05 Å30.77 Å
Translation2.05 Å30.77 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALA3.3.21data scaling
XDSVERSION January 10, 2014 BUILT=20140115data reduction
Coot0.8-pre-4968model building
PDB_EXTRACT3.14data extraction
PHASER2.5.6phasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QOB

2qob


Resolution: 2.047→30.773 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 906 5.02 %
Rwork0.1627 --
obs0.1646 18062 94.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 2.047→30.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 26 186 2397
Biso mean--26.28 29.49 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072269
X-RAY DIFFRACTIONf_angle_d0.9893070
X-RAY DIFFRACTIONf_dihedral_angle_d13.472846
X-RAY DIFFRACTIONf_chiral_restr0.037341
X-RAY DIFFRACTIONf_plane_restr0.005389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0472-2.17540.23741310.18492715X-RAY DIFFRACTION91
2.1754-2.34330.23151450.16712828X-RAY DIFFRACTION95
2.3433-2.5790.21131510.17212824X-RAY DIFFRACTION95
2.579-2.95190.22661550.17572886X-RAY DIFFRACTION96
2.9519-3.71810.18111650.15732896X-RAY DIFFRACTION97
3.7181-30.77610.18441590.15083007X-RAY DIFFRACTION97

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