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- PDB-6fnj: Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase wi... -

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Basic information

Entry
Database: PDB / ID: 6fnj
TitleCrystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with an isomer of NVP-BHG712
ComponentsEphrin type-B receptor 4
KeywordsTRANSFERASE / Inhibitor / Complex / Protein Tyrosine Kinase
Function / homology
Function and homology information


ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase ...ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation / angiogenesis / receptor complex / cell adhesion / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / 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-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / 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 / EGF-like domain signature 2. / 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-DWT / Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.239 Å
AuthorsKudlinzki, D. / Troester, A. / Witt, K. / Linhard, V.L. / Saxena, K. / Schwalbe, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
DKTKL590 Germany
CitationJournal: ChemMedChem / Year: 2018
Title: NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family.
Authors: Troster, A. / Heinzlmeir, S. / Berger, B.T. / Gande, S.L. / Saxena, K. / Sreeramulu, S. / Linhard, V. / Nasiri, A.H. / Bolte, M. / Muller, S. / Kuster, B. / Medard, G. / Kudlinzki, D. / Schwalbe, H.
History
DepositionFeb 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Ephrin type-B receptor 4
B: Ephrin type-B receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0465
Polymers66,9772
Non-polymers1,0693
Water11,638646
1
A: Ephrin type-B receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9922
Polymers33,4881
Non-polymers5031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin type-B receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0543
Polymers33,4881
Non-polymers5662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.820, 87.690, 81.742
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ephrin type-B receptor 4 / Hepatoma transmembrane kinase / Tyrosine-protein kinase TYRO11


Mass: 33488.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB4, HTK, MYK1, TYRO11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P54760, receptor protein-tyrosine kinase
#2: Chemical ChemComp-DWT / 4-methyl-3-[(2-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]-~{N}-[3-(trifluoromethyl)phenyl]benzamide


Mass: 503.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H20F3N7O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 % PEG5000 MME, 0.15 M MgCl2, 15 % Glycerol, 0.1 M TRIS pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.708479 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708479 Å / Relative weight: 1
ReflectionResolution: 1.239→45.34 Å / Num. obs: 210835 / % possible obs: 99.6 % / Redundancy: 6.68 % / Biso Wilson estimate: 27.44 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.084 / Net I/σ(I): 8.14
Reflection shellResolution: 1.239→1.31 Å / Redundancy: 6.43 % / Mean I/σ(I) obs: 0.14 / Num. unique obs: 33525 / CC1/2: 0.114 / % possible all: 98.2

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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: 2VWU

2vwu


Resolution: 1.239→45.336 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 43.18
RfactorNum. reflection% reflection
Rfree0.2244 2143 1.05 %
Rwork0.2096 --
obs0.2089 204142 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.239→45.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 78 648 4878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094501
X-RAY DIFFRACTIONf_angle_d0.9836112
X-RAY DIFFRACTIONf_dihedral_angle_d17.1872756
X-RAY DIFFRACTIONf_chiral_restr0.182654
X-RAY DIFFRACTIONf_plane_restr0.005795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2393-1.26820.65271030.732310136X-RAY DIFFRACTION73
1.2682-1.29990.65541270.709711913X-RAY DIFFRACTION86
1.2999-1.3350.77251420.652513336X-RAY DIFFRACTION96
1.335-1.37430.60011470.583213827X-RAY DIFFRACTION100
1.3743-1.41870.47161460.511113786X-RAY DIFFRACTION100
1.4187-1.46940.43371480.4413833X-RAY DIFFRACTION100
1.4694-1.52820.39391470.388113854X-RAY DIFFRACTION100
1.5282-1.59780.3711470.342713802X-RAY DIFFRACTION99
1.5978-1.6820.34231470.274813843X-RAY DIFFRACTION100
1.682-1.78740.23641480.228213850X-RAY DIFFRACTION100
1.7874-1.92540.24311460.201613888X-RAY DIFFRACTION100
1.9254-2.11920.25361480.198413901X-RAY DIFFRACTION100
2.1192-2.42580.20731480.183213920X-RAY DIFFRACTION100
2.4258-3.05620.2041490.186914018X-RAY DIFFRACTION100
3.0562-45.36650.16091500.153114091X-RAY DIFFRACTION100

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