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- PDB-6q7c: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -

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Basic information

Entry
Database: PDB / ID: 6q7c
TitleCrystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL11
ComponentsEphrin type-A receptor 2
KeywordsTRANSFERASE / Inhibitor / Complex / Protein Tyrosine Kinase
Function / homology
Function and homology information


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / tight junction / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / molecular function activator activity / negative regulation of angiogenesis / skeletal system development / protein localization to plasma membrane / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 2, ligand binding domain / 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. ...Ephrin type-A receptor 2, ligand binding domain / 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 / 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
Chem-HOK / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.049 Å
AuthorsKudlinzki, D. / Troester, A. / Witt, K. / Linhard, V.L. / Gande, S.L. / Saxena, K. / Schwalbe, H.
CitationJournal: To Be Published
Title: Effects of NVP-BHG712 chemical modifications on EPHA2 binding and affinity
Authors: Troester, A. / Kudlinzki, D. / Saxena, K. / Gande, S. / Schwalbe, H.
History
DepositionDec 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0012
Polymers34,4631
Non-polymers5391
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.758, 106.115, 40.301
Angle α, β, γ (deg.)90.00, 108.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 34462.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Chemical ChemComp-HOK / 3-[[4-imidazol-1-yl-6-[(3~{S})-3-oxidanylpiperidin-1-yl]-1,3,5-triazin-2-yl]amino]-4-methyl-~{N}-[3-(trifluoromethyl)phenyl]benzamide


Mass: 538.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25F3N8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 1.93 Å3/Da / Density % sol: 36.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 37.5 % MPD_PEG1000_PEG3350, 100 mM Morpheus Amino Acids Mix, 100 mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.049→38.117 Å / Num. obs: 120259 / % possible obs: 98.6 % / Redundancy: 6.55 % / Biso Wilson estimate: 13.92 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.191 / Net I/σ(I): 5.6
Reflection shellResolution: 1.049→1.11 Å / Redundancy: 5.99 % / Mean I/σ(I) obs: 0.29 / Num. unique obs: 18759 / CC1/2: 0.103 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(dev_3318: ???)refinement
XDSXDSapp 2.0data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FNF

6fnf


Resolution: 1.049→38.117 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.89
RfactorNum. reflection% reflection
Rfree0.2118 2089 1.74 %
Rwork0.1923 --
obs0.1929 119805 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.049→38.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 39 353 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062463
X-RAY DIFFRACTIONf_angle_d0.9623348
X-RAY DIFFRACTIONf_dihedral_angle_d14.9111522
X-RAY DIFFRACTIONf_chiral_restr0.081360
X-RAY DIFFRACTIONf_plane_restr0.005431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0492-1.07360.42051350.4277600X-RAY DIFFRACTION97
1.0736-1.10040.44491370.40537719X-RAY DIFFRACTION97
1.1004-1.13020.37061390.36597867X-RAY DIFFRACTION99
1.1302-1.16350.33661380.33967796X-RAY DIFFRACTION99
1.1635-1.2010.32941380.31397825X-RAY DIFFRACTION99
1.201-1.24390.3081400.29687855X-RAY DIFFRACTION99
1.2439-1.29370.26861400.27177903X-RAY DIFFRACTION100
1.2937-1.35260.29011400.25197880X-RAY DIFFRACTION99
1.3526-1.42390.24431400.23587848X-RAY DIFFRACTION99
1.4239-1.51320.21441390.20217813X-RAY DIFFRACTION99
1.5132-1.630.1811410.1727944X-RAY DIFFRACTION100
1.63-1.7940.17061400.15927901X-RAY DIFFRACTION99
1.794-2.05360.16811400.15097861X-RAY DIFFRACTION99
2.0536-2.58720.19081410.15447930X-RAY DIFFRACTION100
2.5872-38.14170.16731410.14427974X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.17970.03560.24340.64130.18630.361-0.0264-0.0336-0.0189-0.03960.05560.02190.0402-0.01850.00120.1864-0.0159-0.01090.1416-0.01240.2115-90.3097-29.491581.6187
21.47110.3944-1.08251.3838-0.78431.0942-0.03980.0562-0.049-0.14120.0026-0.18550.17560.1070.02640.1718-0.0125-0.00270.1222-0.00090.1569-82.6497-28.868884.0131
30.37710.26560.01080.9857-0.32740.1999-0.02770.0157-0.0566-0.06440.0470.03290.05430.0011-0.01610.11850.0002-0.00020.1038-0.00410.1063-85.4627-18.643784.8325
40.58730.0747-0.07040.46210.16160.4602-0.0017-0.0396-0.0530.012-0.0047-0.01690.05820.03480.01030.09710.00110.00230.10280.00890.0978-81.9803-5.712192.7074
50.82730.01060.32840.6921-0.20470.7754-0.0271-0.05440.0510.03230.0029-0.0025-0.03960.01080.020.11010.0086-0.00010.1098-0.0080.1011-82.00636.357395.0117
63.47050.3865-0.08391.0354-0.21080.8881-0.0866-0.1865-0.0290.0179-0.0328-0.373-0.00810.26790.03760.2243-0.0036-0.01110.22210.00960.2703-63.864314.967689.9676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 599 through 618 )
2X-RAY DIFFRACTION2chain 'A' and (resid 619 through 653 )
3X-RAY DIFFRACTION3chain 'A' and (resid 654 through 712 )
4X-RAY DIFFRACTION4chain 'A' and (resid 713 through 822 )
5X-RAY DIFFRACTION5chain 'A' and (resid 823 through 881 )
6X-RAY DIFFRACTION6chain 'A' and (resid 882 through 896 )

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