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- PDB-7kpl: Crystal structure of hEphB1 in apo form -

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Basic information

Entry
Database: PDB / ID: 7kpl
TitleCrystal structure of hEphB1 in apo form
ComponentsEphrin type-B receptor 1
KeywordsTRANSFERASE / HEPHB1
Function / homology
Function and homology information


skeletal muscle satellite cell activation / negative regulation of satellite cell differentiation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / axon guidance receptor activity / central nervous system projection neuron axonogenesis / immunological synapse formation / filopodium tip / dendritic spine development ...skeletal muscle satellite cell activation / negative regulation of satellite cell differentiation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / axon guidance receptor activity / central nervous system projection neuron axonogenesis / immunological synapse formation / filopodium tip / dendritic spine development / camera-type eye morphogenesis / transmembrane-ephrin receptor activity / dendritic spine morphogenesis / neural precursor cell proliferation / positive regulation of synapse assembly / EPH-Ephrin signaling / Ephrin signaling / establishment of cell polarity / retinal ganglion cell axon guidance / cell-substrate adhesion / detection of temperature stimulus involved in sensory perception of pain / regulation of JNK cascade / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / EPHB-mediated forward signaling / neurogenesis / regulation of ERK1 and ERK2 cascade / cell chemotaxis / axon guidance / modulation of chemical synaptic transmission / receptor protein-tyrosine kinase / early endosome membrane / angiogenesis / protein autophosphorylation / membrane raft / axon / glutamatergic synapse / dendrite / protein-containing complex binding / 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. / Receptor tyrosine kinase class V signature 2. ...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 / EGF-like domain signature 2. / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
Similarity search - Domain/homology
Ephrin type-B receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 Å
AuthorsAhmed, M. / Wang, P. / Sadek, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Identification of tetracycline combinations as EphB1 tyrosine kinase inhibitors for treatment of neuropathic pain.
Authors: Ahmed, M.S. / Wang, P. / Nguyen, N.U.N. / Nakada, Y. / Menendez-Montes, I. / Ismail, M. / Bachoo, R. / Henkemeyer, M. / Sadek, H.A. / Kandil, E.S.
History
DepositionNov 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-B receptor 1


Theoretical massNumber of molelcules
Total (without water)31,8231
Polymers31,8231
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.057, 91.461, 97.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 31823.459 Da / Num. of mol.: 1
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)
References: UniProt: P54762, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium malonate, pH 4.6, 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8602 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.36 / Net I/σ(I): 9.69
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 1.16 / Num. unique obs: 833 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3zfx

3zfx


Resolution: 2.705→48.718 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 403 4.8 %
Rwork0.1997 7998 -
obs0.202 8401 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.24 Å2 / Biso mean: 35.803 Å2 / Biso min: 14.75 Å2
Refinement stepCycle: final / Resolution: 2.705→48.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 36 2092
Biso mean---36.78 -
Num. residues----256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.705-3.09610.25271120.2252253695
3.0961-3.90060.25841620.2021264499
3.9006-48.70.24121290.1894281899

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