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

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Basic information

Entry
Database: PDB / ID: 6hex
TitleCrystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATMM006
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 / regulation of blood vessel endothelial cell migration / positive regulation of bicellular tight junction assembly ...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 / regulation of blood vessel endothelial cell migration / positive regulation of bicellular tight junction assembly / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / response to growth factor / tight junction / regulation of lamellipodium assembly / activation of GTPase activity / 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 / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / ephrin receptor signaling pathway / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / vasculogenesis / regulation of ERK1 and ERK2 cascade / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / 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 / neuron differentiation / ruffle membrane / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / virus receptor activity / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / protein phosphorylation / 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-G02 / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.413 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
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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)34,9672
Polymers34,4631
Non-polymers5041
Water5,603311
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 area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.831, 107.218, 40.533
Angle α, β, γ (deg.)90.00, 108.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin type-A receptor 2


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
#2: Chemical ChemComp-G02 / 4-methyl-3-[(1-methyl-6-pyrazin-2-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]-~{N}-[3-(trifluoromethyl)phenyl]benzamide


Mass: 504.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H19F3N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 37.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 37.5 % MPD/PEG1000/PEG3350 (MD), 0.1 M Amino Acids Mix (MD), 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.41→38.38 Å / Num. obs: 47501 / % possible obs: 93.6 % / Redundancy: 7.05 % / Biso Wilson estimate: 19.46 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.112 / Net I/σ(I): 10.76
Reflection shellResolution: 1.41→1.5 Å / Redundancy: 6.87 % / Mean I/σ(I) obs: 2.82 / Num. unique obs: 6570 / CC1/2: 0.843 / % possible all: 79.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSXDSapp 2.0data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FNF

6fnf


Resolution: 1.413→31.086 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.23
RfactorNum. reflection% reflection
Rfree0.1785 2099 4.42 %
Rwork0.1593 --
obs0.1599 47496 93.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.413→31.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 37 312 2490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122345
X-RAY DIFFRACTIONf_angle_d1.0543181
X-RAY DIFFRACTIONf_dihedral_angle_d18.8631426
X-RAY DIFFRACTIONf_chiral_restr0.235335
X-RAY DIFFRACTIONf_plane_restr0.006401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4128-1.44560.2367990.21072141X-RAY DIFFRACTION66
1.4456-1.48180.2351300.18922810X-RAY DIFFRACTION88
1.4818-1.52180.20071380.18132999X-RAY DIFFRACTION94
1.5218-1.56660.22051440.17643102X-RAY DIFFRACTION95
1.5666-1.61720.18431410.17473050X-RAY DIFFRACTION95
1.6172-1.6750.19041410.18153054X-RAY DIFFRACTION95
1.675-1.7420.20051420.1663064X-RAY DIFFRACTION96
1.742-1.82130.17491440.16533117X-RAY DIFFRACTION96
1.8213-1.91730.2111430.16143096X-RAY DIFFRACTION96
1.9173-2.03740.17951440.1633108X-RAY DIFFRACTION96
2.0374-2.19470.15831450.14923138X-RAY DIFFRACTION97
2.1947-2.41550.17681460.15623147X-RAY DIFFRACTION98
2.4155-2.76480.18521450.16193150X-RAY DIFFRACTION98
2.7648-3.48260.18271480.14723187X-RAY DIFFRACTION98
3.4826-31.09380.14871490.143234X-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)
10.2593-0.1635-0.27810.32090.22890.52820.0444-0.15840.3294-0.17440.1642-0.1854-0.00470.1239-0.21090.2816-0.0319-0.00260.2042-0.08090.3515-56.0639-32.73680.5295
21.17350.0248-0.66050.6482-0.72391.3749-0.0080.0318-0.0076-0.18290.117-0.37620.18540.4046-0.14950.2819-0.0080.0360.1588-0.06380.273-49.9698-30.858885.1648
30.9885-0.45110.61243.0694-2.19034.4143-0.1041-0.10130.09370.21220.2050.3514-0.0829-0.1176-0.24450.22650.0364-0.00150.12660.00990.3083-60.2188-27.98194.4554
40.43980.0278-0.04830.8249-0.0980.3821-0.00590.0476-0.0843-0.08030.00680.0320.12210.03330.00570.144-0.0034-0.0030.1139-0.00920.1136-50.7101-18.903282.8001
50.68570.1239-0.01890.61970.09960.5427-0.0136-0.0712-0.02330.02560-0.0260.03650.03180.01090.08670.00330.00420.10940.01170.0883-49.5555-7.378994.9864
61.0009-0.01180.3470.9241-0.18891.2062-0.0271-0.0380.1161-0.03130.00570.0284-0.06040.00810.01490.10550.006-0.00240.0960.0010.1069-51.62335.146493.0365
73.96040.6419-0.16371.217-0.10620.3220.013-0.2233-0.0379-0.0318-0.0038-0.4444-0.04420.18490.06330.2305-0.00530.00770.21090.00910.3383-31.799512.398491.0552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 605 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 831 )
6X-RAY DIFFRACTION6chain 'A' and (resid 832 through 881 )
7X-RAY DIFFRACTION7chain 'A' and (resid 882 through 896 )

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