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- PDB-2qoc: Human EphA3 kinase domain, phosphorylated, AMP-PNP bound structure -

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Basic information

Entry
Database: PDB / ID: 2qoc
TitleHuman EphA3 kinase domain, phosphorylated, AMP-PNP bound structure
ComponentsEphrin receptor
KeywordsTRANSFERASE / receptor tyrosine kinase / structural genomics / AMP-PNP / Structural Genomics Consortium / SGC / ATP-binding / Membrane / Nucleotide-binding / Phosphorylation / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


fasciculation of sensory neuron axon / fasciculation of motor neuron axon / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of GTPase activity / regulation of focal adhesion assembly ...fasciculation of sensory neuron axon / fasciculation of motor neuron axon / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / regulation of epithelial to mesenchymal transition / ephrin receptor activity / negative regulation of endocytosis / EPH-Ephrin signaling / regulation of GTPase activity / regulation of focal adhesion assembly / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / cellular response to retinoic acid / axon guidance / regulation of microtubule cytoskeleton organization / peptidyl-tyrosine phosphorylation / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / positive regulation of neuron projection development / receptor protein-tyrosine kinase / 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 ...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 / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / BETA-MERCAPTOETHANOL / Ephrin type-A receptor 3 / Ephrin type-A receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsDavis, T. / Walker, J.R. / Newman, E.M. / Mackenzie, F. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Davis, T. / Walker, J.R. / Newman, E.M. / Mackenzie, F. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2008
Title: Autoregulation by the Juxtamembrane Region of the Human Ephrin Receptor Tyrosine Kinase A3 (EphA3).
Authors: Davis, T.L. / Walker, J.R. / Loppnau, P. / Butler-Cole, C. / Allali-Hassani, A. / Dhe-Paganon, S.
History
DepositionJul 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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 / 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: Ephrin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2025
Polymers38,5691
Non-polymers6334
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.790, 38.337, 76.439
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin receptor


Mass: 38569.102 Da / Num. of mol.: 1 / Fragment: Kinase domain: Residues 606-947
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Placenta / Gene: EPHA3 / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6P4R6, UniProt: P29320*PLUS, receptor protein-tyrosine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mg/mL Protein, 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 84007 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Χ2: 1.024 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.25-1.293.30.2582760.66698.6
1.29-1.353.50.20283560.66199.8
1.35-1.413.50.15783460.68999.6
1.41-1.483.50.11583840.74299.9
1.48-1.573.60.08683770.83299.9
1.57-1.73.60.0783840.98799.8
1.7-1.873.60.05784031.20699.9
1.87-2.143.70.04984681.455100
2.14-2.693.70.04384711.37799.9
2.69-503.50.03985421.50298.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QOB

2qob


Resolution: 1.25→27.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.63 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 4110 5 %RANDOM
Rwork0.169 ---
obs0.17 82459 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.324 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 42 427 2952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222597
X-RAY DIFFRACTIONr_bond_other_d0.0010.021800
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9873564
X-RAY DIFFRACTIONr_angle_other_deg0.8634419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.175349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92323.694111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64115476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1811521
X-RAY DIFFRACTIONr_chiral_restr0.070.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022970
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02537
X-RAY DIFFRACTIONr_nbd_refined0.2330.2575
X-RAY DIFFRACTIONr_nbd_other0.1820.22027
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21335
X-RAY DIFFRACTIONr_nbtor_other0.0820.21272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2304
X-RAY DIFFRACTIONr_metal_ion_refined0.2940.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.234
X-RAY DIFFRACTIONr_mcbond_it0.761.52099
X-RAY DIFFRACTIONr_mcbond_other0.1211.5630
X-RAY DIFFRACTIONr_mcangle_it0.90222610
X-RAY DIFFRACTIONr_scbond_it1.46631186
X-RAY DIFFRACTIONr_scangle_it1.94.5942
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 273 -
Rwork0.238 5208 -
all-5481 -
obs--88.09 %

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