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- PDB-6q7g: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -

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Basic information

Entry
Database: PDB / ID: 6q7g
TitleCrystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATHA01
ComponentsEphrin type-A receptor 2
KeywordsTRANSFERASE / Inhibitor / Complex / Protein Tyrosine Kinase
Function / homology
Function and homology information


notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / response to growth factor / activation of GTPase activity / tight junction / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / regulation of ERK1 and ERK2 cascade / negative regulation of angiogenesis / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / cadherin binding / 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 / Growth factor receptor cysteine-rich domain superfamily / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-HO8 / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.047 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

Downloads & links

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Assembly

Deposited unit
A: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9872
Polymers34,4631
Non-polymers5241
Water5,405300
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 area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.781, 107.384, 40.552
Angle α, β, γ (deg.)90.00, 108.66, 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-HO8 / 3-[(4-imidazol-1-yl-6-morpholin-4-yl-1,3,5-triazin-2-yl)amino]-4-methyl-~{N}-[3-(trifluoromethyl)phenyl]benzamide


Mass: 524.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23F3N8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 37.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 % PEG3350, 100 mM Morpheus Amino Acids Mix, 100 mM Morpheus Buffer System 3 (Tris/Bicine)

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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: 1.047→36.175 Å / Num. obs: 115942 / % possible obs: 93.2 % / Redundancy: 6.93 % / Biso Wilson estimate: 15.69 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.127 / Net I/σ(I): 7.06
Reflection shellResolution: 1.047→1.11 Å / Redundancy: 6.59 % / Mean I/σ(I) obs: 0.29 / Num. unique obs: 17627 / CC1/2: 0.102 / % possible all: 87.8

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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: 1.047→36.175 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.97
RfactorNum. reflection% reflection
Rfree0.2009 2096 1.81 %
Rwork0.1868 --
obs0.1872 115662 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.047→36.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 38 300 2521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062453
X-RAY DIFFRACTIONf_angle_d0.9673330
X-RAY DIFFRACTIONf_dihedral_angle_d16.71515
X-RAY DIFFRACTIONf_chiral_restr0.087351
X-RAY DIFFRACTIONf_plane_restr0.006430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0472-1.07160.47751230.42776643X-RAY DIFFRACTION82
1.0716-1.09840.39071340.39477253X-RAY DIFFRACTION89
1.0984-1.12810.37131370.34997403X-RAY DIFFRACTION91
1.1281-1.16120.34911360.32827408X-RAY DIFFRACTION91
1.1612-1.19870.27831370.30817437X-RAY DIFFRACTION92
1.1987-1.24160.31961380.29047438X-RAY DIFFRACTION92
1.2416-1.29130.26731390.27467559X-RAY DIFFRACTION93
1.2913-1.35010.27061420.25447693X-RAY DIFFRACTION94
1.3501-1.42120.22361410.23157638X-RAY DIFFRACTION94
1.4212-1.51030.25851400.20817623X-RAY DIFFRACTION94
1.5103-1.62690.18751450.18027824X-RAY DIFFRACTION96
1.6269-1.79060.16551440.16777818X-RAY DIFFRACTION96
1.7906-2.04970.18871440.16697819X-RAY DIFFRACTION96
2.0497-2.58230.18121470.16257979X-RAY DIFFRACTION98
2.5823-36.19660.1591490.14988031X-RAY DIFFRACTION98
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)
10.00870.0125-0.00160.2395-0.15340.4401-0.0666-0.20470.3744-0.00940.00260.06050.2481-0.0651-0.05090.2625-0.07750.00190.2222-0.11240.3144-89.5964-29.51981.7295
20.1847-0.0182-0.14260.21580.05470.077-0.10110.0469-0.146-0.04340.0596-0.18550.14190.1129-0.00130.2538-0.03570.01230.1709-0.01740.202-82.557-28.646284.8181
30.0334-0.02960.03660.0555-0.05210.0196-0.0507-0.0370.11720.08210.02840.2269-0.07770.0370.00050.24160.0295-0.03040.12710.00750.2593-92.7777-25.479394.5976
40.40960.0625-0.29890.0612-0.0330.22170.04220.1502-0.04650.0268-0.03860.24830.1522-0.31350.10330.1872-0.0801-0.02950.1393-0.02430.15-91.7186-22.437383.7184
50.2905-0.0212-0.17010.52470.04290.5481-0.01160.0352-0.0104-0.03890.01220.00590.0328-0.020300.1123-0.00550.00130.12020.00080.1086-82.6267-8.404885.3453
60.07190.06260.02350.1438-0.09690.1060.0353-0.0828-0.06350.0451-0.0285-0.04570.0616-0.004600.1373-0.00030.00060.16750.01750.1226-83.7935-8.4483103.4136
70.2844-0.0228-0.04730.52590.05090.2476-0.0635-0.1159-0.03350.03860.0242-0.07010.03930.0834-0.00020.10850.0122-0.00450.15480.01220.1197-76.2213-1.062499.243
80.1035-0.17410.13470.2806-0.12270.2648-0.0721-0.12220.0806-0.01540.00990.008-0.0263-0.012600.12680.0062-0.00150.1373-0.00360.1285-81.97326.993898.617
90.0041-0.02280.02990.1272-0.01950.10450.00740.08210.0911-0.06870.04970.1511-0.157-0.1686-0.01920.18490.0076-0.02260.14090.02870.1687-89.33888.470583.5103
100.10090.0396-0.02460.0181-0.0050.0129-0.0532-0.13450.0214-0.0760.0621-0.4947-0.03480.18750.00040.2621-0.0056-0.00830.2458-0.00720.4374-64.216514.939390.9571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 601 through 618 )
2X-RAY DIFFRACTION2chain 'A' and (resid 619 through 653 )
3X-RAY DIFFRACTION3chain 'A' and (resid 654 through 669 )
4X-RAY DIFFRACTION4chain 'A' and (resid 670 through 687 )
5X-RAY DIFFRACTION5chain 'A' and (resid 688 through 755 )
6X-RAY DIFFRACTION6chain 'A' and (resid 756 through 795 )
7X-RAY DIFFRACTION7chain 'A' and (resid 796 through 831 )
8X-RAY DIFFRACTION8chain 'A' and (resid 832 through 863 )
9X-RAY DIFFRACTION9chain 'A' and (resid 864 through 881 )
10X-RAY DIFFRACTION10chain 'A' and (resid 882 through 896 )

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