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- PDB-6q7d: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -

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Basic information

Entry
Database: PDB / ID: 6q7d
TitleCrystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL13
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 / lens fiber cell morphogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / leading edge membrane ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / lens fiber cell morphogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / 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 / tight junction / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / hepatocyte growth factor receptor activity / platelet-derived growth factor beta-receptor activity / placental growth factor receptor activity / brain-derived neurotrophic factor receptor activity / boss receptor activity / platelet-derived growth factor alpha-receptor activity / RHOU GTPase cycle / epidermal growth factor receptor activity / lamellipodium membrane / macrophage colony-stimulating factor receptor activity / protein tyrosine kinase collagen receptor activity / stem cell factor receptor activity / insulin-like growth factor receptor activity / transmembrane-ephrin receptor activity / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / GPI-linked ephrin receptor activity / vascular endothelial growth factor receptor activity / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / fibroblast growth factor receptor activity / regulation of ERK1 and ERK2 cascade / insulin receptor activity / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / negative regulation of angiogenesis / molecular function activator activity / 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 / neuron differentiation / 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 / 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 / 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-HOT / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.978 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)35,0012
Polymers34,4631
Non-polymers5391
Water5,945330
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 area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.725, 107.160, 40.463
Angle α, β, γ (deg.)90.00, 108.42, 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-HOT / 3-[[4-imidazol-1-yl-6-(4-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.: 330 / 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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 % PEG 3350, 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: 0.978→36.142 Å / Num. obs: 141511 / % possible obs: 93.2 % / Redundancy: 6.69 % / Biso Wilson estimate: 13.92 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.109 / Net I/σ(I): 7.56
Reflection shellResolution: 0.978→1.04 Å / Mean I/σ(I) obs: 0.24 / Num. unique obs: 19879 / CC1/2: 0.101 / % possible all: 81

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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: 0.978→36.142 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.91
RfactorNum. reflection% reflection
Rfree0.2071 2083 1.48 %
Rwork0.1855 --
obs0.1861 140587 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.978→36.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 39 330 2565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072473
X-RAY DIFFRACTIONf_angle_d1.1673362
X-RAY DIFFRACTIONf_dihedral_angle_d18.531528
X-RAY DIFFRACTIONf_chiral_restr0.088356
X-RAY DIFFRACTIONf_plane_restr0.006436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9781-1.00080.4183860.45485886X-RAY DIFFRACTION59
1.0008-1.02590.40191330.41998891X-RAY DIFFRACTION89
1.0259-1.05360.37791380.39459132X-RAY DIFFRACTION92
1.0536-1.08460.3291390.3519204X-RAY DIFFRACTION93
1.0846-1.11960.30681390.31299267X-RAY DIFFRACTION93
1.1196-1.15960.27871410.27869310X-RAY DIFFRACTION94
1.1596-1.20610.24631410.2539388X-RAY DIFFRACTION94
1.2061-1.2610.2411420.23619432X-RAY DIFFRACTION95
1.261-1.32740.24251430.21699456X-RAY DIFFRACTION95
1.3274-1.41060.21861440.19969604X-RAY DIFFRACTION96
1.4106-1.51950.18751450.17949595X-RAY DIFFRACTION97
1.5195-1.67240.17781470.16059763X-RAY DIFFRACTION98
1.6724-1.91440.18081470.1669786X-RAY DIFFRACTION98
1.9144-2.41190.18311490.16429855X-RAY DIFFRACTION99
2.4119-36.16630.18781490.15489935X-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)
10.04040.03290.0580.1275-0.11080.2961-0.0474-0.08150.3172-0.02660.08020.07910.1654-0.16160.02540.2558-0.05920.01760.1853-0.0890.3172-89.5343-29.346281.9043
20.1817-0.0635-0.13250.18940.08890.0914-0.08170.0564-0.1304-0.07680.1226-0.15690.1920.0496-0.00290.2575-0.03320.02380.1408-0.01960.1959-82.1948-28.840584.9705
30.07090.010.01020.03050.00610.00650.017-0.08140.02070.13020.0660.382-0.04460.02740.00140.22760.01230.00170.14880.0230.2734-92.3118-25.382694.4337
40.25430.0108-0.15990.2538-0.070.5191-0.04840.0873-0.0271-0.10760.0237-0.00220.10130.004-0.00070.1306-0.0076-0.00560.1096-0.00960.1186-82.0209-16.000182.5887
50.33040.0288-0.08330.44030.26790.2063-0.01180.0365-0.0187-0.0390.0160.02540.0317-0.03590.00120.09620.0020.00080.11430.0050.0994-85.2631-6.151186.5783
60.05390.0586-0.0210.1235-0.11010.0890.0276-0.107-0.04190.0342-0.0154-0.04820.04960.025500.1261-0.0023-0.00580.15470.01520.1061-83.1467-8.5537103.5164
70.1788-0.0219-0.05690.48690.03850.2404-0.0644-0.1118-0.02470.02010.0198-0.04980.04670.0885-0.00460.09520.0129-0.00450.1420.01420.1011-75.4663-1.087499.1181
80.0991-0.11810.15150.3192-0.06680.2709-0.0468-0.1350.07070.03340.0074-0.0044-0.02680.0078-0.00010.12130.0056-0.00320.1309-0.00490.1237-81.21476.95498.5074
90.1205-0.12590.080.17950.00750.23760.02050.12360.1482-0.02750.02120.194-0.2394-0.1712-0.07360.17060.0092-0.02270.1310.0340.1517-88.59848.229483.8027
100.02270.0086-0.04360.0483-0.01930.0696-0.11050.09480.0414-0.25710.0272-0.5666-0.05620.3642-0.00730.2048-0.02410.02010.28720.02050.4408-63.379715.005490.7656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 600 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 712 )
5X-RAY DIFFRACTION5chain 'A' and (resid 713 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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