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- PDB-5mjb: Kinase domain of human EphB1, G703C mutant, covalently bound to a... -

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Basic information

Entry
Database: PDB / ID: 5mjb
TitleKinase domain of human EphB1, G703C mutant, covalently bound to a quinazoline-based inhibitor
ComponentsEphrin type-B receptor 1
KeywordsTRANSFERASE / Receptor tyrosine kinase / kinase domain / Inhibitor / covalent
Function / homology
Function and homology information


skeletal muscle satellite cell activation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / negative regulation of satellite cell differentiation / axon guidance receptor activity / central nervous system projection neuron axonogenesis / immunological synapse formation / filopodium tip / dendritic spine development ...skeletal muscle satellite cell activation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / negative regulation of satellite cell differentiation / axon guidance receptor activity / central nervous system projection neuron axonogenesis / immunological synapse formation / filopodium tip / dendritic spine development / camera-type eye morphogenesis / dendritic spine morphogenesis / positive regulation of synapse assembly / regulation of JNK cascade / EPH-Ephrin signaling / neural precursor cell proliferation / Ephrin signaling / retinal ganglion cell axon guidance / establishment of cell polarity / cell-substrate adhesion / detection of temperature stimulus involved in sensory perception of pain / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / neurogenesis / EPHB-mediated forward signaling / axon guidance / cell chemotaxis / modulation of chemical synaptic transmission / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / protein autophosphorylation / early endosome membrane / angiogenesis / membrane raft / axon / dendrite / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM 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. ...Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM 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 / 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-7O3 / Ephrin type-B receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsKung, A. / Schimpl, M. / Chen, Y.-C. / Overman, R.C. / Zhang, C.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: A Chemical-Genetic Approach to Generate Selective Covalent Inhibitors of Protein Kinases.
Authors: Kung, A. / Schimpl, M. / Ekanayake, A. / Chen, Y.C. / Overman, R. / Zhang, C.
History
DepositionNov 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-B receptor 1
B: Ephrin type-B receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0149
Polymers69,8072
Non-polymers1,2077
Water3,963220
1
A: Ephrin type-B receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5555
Polymers34,9041
Non-polymers6514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ephrin type-B receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4594
Polymers34,9041
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.200, 102.200, 157.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1058-

HOH

21A-1092-

HOH

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Components

#1: Protein Ephrin type-B receptor 1 / ELK / EPH tyrosine kinase 2 / EPH-like kinase 6 / hEK6 / Neuronally-expressed EPH-related tyrosine ...ELK / EPH tyrosine kinase 2 / EPH-like kinase 6 / hEK6 / Neuronally-expressed EPH-related tyrosine kinase / NET / Tyrosine-protein kinase receptor EPH-2


Mass: 34903.703 Da / Num. of mol.: 2 / Mutation: G703C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB1, ELK, EPHT2, HEK6, NET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: P54762, receptor protein-tyrosine kinase
#2: Chemical ChemComp-7O3 / 2-chloranyl-~{N}-[4-[(2-chloranyl-5-oxidanyl-phenyl)amino]quinazolin-7-yl]ethanamide


Mass: 363.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12Cl2N4O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.42 Å3/Da / Density % sol: 64.08 % / Description: hexagonal plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18 % PEG3350, 0.1-0.2 M ammonium sulfate and 0.1 M PCTP (Sodium propionate, Sodium cacodylate trihydrate, Bis-Tris propane) buffer pH 6-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.23→58.84 Å / Num. obs: 47109 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 51.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.2
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.707 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.622 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZFX

3zfx


Resolution: 2.23→58.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.952 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2232 4.8 %RANDOM
Rwork0.198 ---
obs0.199 46452 98.7 %-
Displacement parametersBiso mean: 59.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.8447 Å20 Å20 Å2
2--0.8447 Å20 Å2
3----1.6895 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.23→58.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 135 220 4709
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014582HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.066205HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1586SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes659HARMONIC5
X-RAY DIFFRACTIONt_it4582HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion18.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion577SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5267SEMIHARMONIC4
LS refinement shellResolution: 2.23→2.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 171 5.07 %
Rwork0.308 3201 -
all0.309 3372 -
obs--97.43 %
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)
12.31980.11330.21082.011-0.31482.4874-0.2232-0.1773-0.09340.19160.2175-0.46740.08020.02160.0057-0.22220.0709-0.006-0.1463-0.0412-0.063-1.857439.7546-3.0785
22.50280.35450.80471.32810.15961.4634-0.1315-0.17650.09260.11980.21130.2605-0.0888-0.1992-0.0798-0.23670.05830.05390.02230.1208-0.1116-33.238740.0775-6.3115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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