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- PDB-6q7b: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -

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Basic information

Entry
Database: PDB / ID: 6q7b
TitleCrystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL09
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-HO5 / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.009 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)34,9872
Polymers34,4631
Non-polymers5241
Water5,675315
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 area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.800, 106.807, 40.402
Angle α, β, γ (deg.)90.00, 108.74, 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-HO5 / 3-[[4-imidazol-1-yl-6-[(3~{S})-3-oxidanylpyrrolidin-1-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.: 315 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 37.5 % MPD_PEG1000_PEG3350 (Precipitant Mix 4 Morpheus), 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: 1.009→31.102 Å / Num. obs: 124435 / % possible obs: 89.9 % / Redundancy: 7.07 % / Biso Wilson estimate: 14.38 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.138 / Net I/σ(I): 7.16
Reflection shellResolution: 1.009→1.07 Å / Redundancy: 6.74 % / Mean I/σ(I) obs: 0.26 / Num. unique obs: 18978 / CC1/2: 0.1 / % possible all: 85

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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: 1.009→31.102 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.53
RfactorNum. reflection% reflection
Rfree0.2025 2085 1.69 %
Rwork0.1867 --
obs0.1871 123523 89.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.009→31.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 38 315 2577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062421
X-RAY DIFFRACTIONf_angle_d1.0143283
X-RAY DIFFRACTIONf_dihedral_angle_d16.0171491
X-RAY DIFFRACTIONf_chiral_restr0.085352
X-RAY DIFFRACTIONf_plane_restr0.006421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0089-1.03240.47121230.45667165X-RAY DIFFRACTION80
1.0324-1.05820.43371320.42887686X-RAY DIFFRACTION85
1.0582-1.08680.44341340.40987785X-RAY DIFFRACTION87
1.0868-1.11880.39691370.3487976X-RAY DIFFRACTION88
1.1188-1.15490.34431370.31758002X-RAY DIFFRACTION89
1.1549-1.19620.26761380.2898009X-RAY DIFFRACTION89
1.1962-1.24410.27161360.27547907X-RAY DIFFRACTION88
1.2441-1.30070.27131410.25688263X-RAY DIFFRACTION91
1.3007-1.36930.25431410.23468161X-RAY DIFFRACTION91
1.3693-1.45510.24821400.21028166X-RAY DIFFRACTION91
1.4551-1.56740.18981420.18338263X-RAY DIFFRACTION91
1.5674-1.72510.19081450.16528451X-RAY DIFFRACTION94
1.7251-1.97470.18651430.15998346X-RAY DIFFRACTION93
1.9747-2.48780.17431470.15568579X-RAY DIFFRACTION95
2.4878-31.11640.1571490.14398679X-RAY DIFFRACTION95
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)
10.20620.03590.14560.1073-0.09470.3020.0245-0.2360.0953-0.06070.07360.01730.0713-0.13770.05340.1986-0.0138-0.00940.1561-0.0520.2333-87.9067-29.062884.648
20.1591-0.01680.030.16980.13940.1217-0.12290.0629-0.0725-0.12570.1468-0.15630.1379-0.1475-0.00190.2009-0.03770.02640.1237-0.01440.1642-83.7994-28.976482.2415
30.05520.02320.0180.02190.01870.0231-0.0553-0.03230.07660.00480.03270.2614-0.0995-0.0530.00090.17030.0099-0.0060.14510.00920.2269-92.8962-25.217994.0774
40.18380.1273-0.02610.3932-0.03810.23820.00360.0169-0.0065-0.03620.00650.00860.02720.001500.1035-0.0014-0.00050.10510.00010.1044-84.0461-11.496584.1246
50.31470.02460.13460.2746-0.02340.18460.0071-0.0623-0.02350.02280.0036-0.02680.04020.036100.10010.0021-0.00060.12720.00880.104-78.5204-4.2828100.251
60.2277-0.05010.10360.425-0.11490.2292-0.024-0.05050.049-0.0139-0.00410.0194-0.01920.0002-00.11640.0058-0.00530.12180.00430.1119-83.65897.639192.9641
70.08650.01-0.04590.00310.00060.0199-0.0857-0.0901-0.0309-0.0602-0.0074-0.2654-0.00040.078-0.00040.1866-0.0026-0.01580.19080.0420.287-63.992615.026290.5021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 599 through 626 )
2X-RAY DIFFRACTION2chain 'A' and (resid 627 through 653 )
3X-RAY DIFFRACTION3chain 'A' and (resid 654 through 669 )
4X-RAY DIFFRACTION4chain 'A' and (resid 670 through 755 )
5X-RAY DIFFRACTION5chain 'A' and (resid 756 through 831 )
6X-RAY DIFFRACTION6chain 'A' and (resid 832 through 881 )
7X-RAY DIFFRACTION7chain 'A' and (resid 882 through 896 )

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