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- PDB-6q7f: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -

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Basic information

Entry
Database: PDB / ID: 6q7f
TitleCrystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL18
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-HNZ / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.204 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)34,9862
Polymers34,4631
Non-polymers5241
Water5,134285
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 area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.671, 107.062, 40.524
Angle α, β, γ (deg.)90.00, 108.83, 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-HNZ / 3-[(4-imidazol-1-yl-6-piperazin-1-yl-1,3,5-triazin-2-yl)amino]-4-methyl-~{N}-[3-(trifluoromethyl)phenyl]benzamide


Mass: 523.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24F3N9O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 37.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 37.5 % MPD_PEG1000_PEG3350, 125 mM Morpheus Carboxylic 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: 1.204→38.355 Å / Num. obs: 76625 / % possible obs: 94.2 % / Redundancy: 6.98 % / Biso Wilson estimate: 19.71 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.158 / Net I/σ(I): 6.84
Reflection shellResolution: 1.204→1.28 Å / Redundancy: 6.74 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 11339 / CC1/2: 0.104 / % possible all: 86.5

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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: 1.204→38.355 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.92
RfactorNum. reflection% reflection
Rfree0.2104 2099 2.74 %
Rwork0.1868 --
obs0.1872 76605 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.204→38.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 38 285 2454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132353
X-RAY DIFFRACTIONf_angle_d1.0623196
X-RAY DIFFRACTIONf_dihedral_angle_d17.2881449
X-RAY DIFFRACTIONf_chiral_restr0.352337
X-RAY DIFFRACTIONf_plane_restr0.006407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2035-1.23150.37531140.40724058X-RAY DIFFRACTION77
1.2315-1.26230.36091380.38294891X-RAY DIFFRACTION93
1.2623-1.29650.38861380.36784908X-RAY DIFFRACTION94
1.2965-1.33460.37331380.34964887X-RAY DIFFRACTION94
1.3346-1.37770.34361400.32624985X-RAY DIFFRACTION94
1.3777-1.42690.34441400.30114962X-RAY DIFFRACTION94
1.4269-1.48410.31521400.28354946X-RAY DIFFRACTION94
1.4841-1.55160.26461420.24875040X-RAY DIFFRACTION96
1.5516-1.63340.22541420.2215049X-RAY DIFFRACTION96
1.6334-1.73580.19591420.19765050X-RAY DIFFRACTION96
1.7358-1.86980.21751440.17825098X-RAY DIFFRACTION96
1.8698-2.05790.20471420.16985053X-RAY DIFFRACTION96
2.0579-2.35570.18011460.15375177X-RAY DIFFRACTION98
2.3557-2.96770.16411470.16645203X-RAY DIFFRACTION99
2.9677-38.37460.1861460.14325199X-RAY DIFFRACTION97
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)
10.1460.0345-0.12080.874-0.0250.31160.0011-0.2275-0.0495-0.04230.1167-0.06370.18310.10080.00160.254-0.01960.0010.2557-0.09140.2706-83.3402-29.182882.7303
20.26530.1893-0.23380.50640.23070.5791-0.03190.0210.0017-0.22170.2489-0.20150.29310.26660.00370.3067-0.0090.02060.1851-0.0330.2118-85.1698-29.572284.5052
30.10830.06350.13390.03260.0410.23940.0468-0.03830.09230.31280.23620.4662-0.44080.0450.05680.30350.04890.02290.16960.03640.3396-93.199-25.496594.2585
40.0406-0.0187-0.11470.14130.1540.1666-0.00330.047-0.0617-0.19570.02210.37820.1039-0.06970.00020.1914-0.0154-0.01450.1279-0.00170.1894-91.7818-22.288483.5534
50.4848-0.0896-0.16050.03760.01550.0177-0.05540.0089-0.031-0.18880.0344-0.06110.14680.0685-0.00080.1691-0.0135-0.00180.1475-0.00420.1423-76.9834-12.218582.1737
60.63580.0513-0.06690.53190.3050.1985-0.0060.0038-0.008-0.05160.01030.0520.0443-0.00940.00060.1197-0.00390.00790.1430.00320.1174-86.306-6.019587.1601
70.61540.17850.10390.2918-0.10850.09450.0356-0.1133-0.05250.0399-0.0218-0.02560.0432-0.004900.1689-0.00460.00250.17340.01880.1236-84.8878-8.2222101.8362
80.2340.1014-0.1230.3619-0.04990.4117-0.0171-0.05040.0169-0.0111-0.0023-0.0610.00640.0621-00.111-0.00250.00520.1620.0110.139-76.5412-0.997795.5633
90.5026-0.170500.78160.29040.1155-0.0246-0.11540.06110.2342-0.0249-0.145-0.20510.0407-0.00010.1567-0.0038-0.02040.2060.00390.1641-74.16283.8357102.7132
100.09990.02280.12310.1498-0.09330.2439-0.0582-0.12910.117-0.0112-0.01160.0031-0.0614-0.0399-0.00020.14060.0027-0.01210.1621-0.00740.1585-86.22736.811799.0007
110.0476-0.03690.03460.0880.04340.1030.01960.06810.1433-0.13080.00350.2501-0.0603-0.04510.00050.1827-0.0029-0.02230.15250.02490.1836-89.31418.254184.1004
120.2720.0885-0.1210.0593-0.13240.1313-0.1181-0.0287-0.136-0.10850.0652-0.2929-0.0350.1226-0.00150.254-0.00680.01840.22310.02280.3594-64.384115.015591.033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 605 through 632 )
2X-RAY DIFFRACTION2chain 'A' and (resid 633 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 712 )
6X-RAY DIFFRACTION6chain 'A' and (resid 713 through 752 )
7X-RAY DIFFRACTION7chain 'A' and (resid 753 through 795 )
8X-RAY DIFFRACTION8chain 'A' and (resid 796 through 822 )
9X-RAY DIFFRACTION9chain 'A' and (resid 823 through 843 )
10X-RAY DIFFRACTION10chain 'A' and (resid 844 through 863 )
11X-RAY DIFFRACTION11chain 'A' and (resid 864 through 881 )
12X-RAY DIFFRACTION12chain 'A' and (resid 882 through 896 )

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