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- PDB-6umw: Crystal structure of hEphB1 bound with chlortetracycline -

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Basic information

Entry
Database: PDB / ID: 6umw
TitleCrystal structure of hEphB1 bound with chlortetracycline
ComponentsEphrin type-B receptor 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / hEphB1 / Chlortetracycline / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
7-CHLOROTETRACYCLINE / Ephrin type-B receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.982 Å
AuthorsAhmed, M. / Wang, P. / Sadek, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
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
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8482
Polymers34,3691
Non-polymers4791
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-2 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.932, 91.090, 96.995
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: 34369.180 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 602-896)
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: Chemical ChemComp-CTC / 7-CHLOROTETRACYCLINE


Mass: 478.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23ClN2O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 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: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 21042 / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 17.9
Reflection shellResolution: 1.98→2.05 Å / Rmerge(I) obs: 0.59 / Num. unique obs: 2074

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ZFX

3zfx


Resolution: 1.982→41.226 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1027 4.9 %
Rwork0.1815 19948 -
obs0.1836 20975 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.14 Å2 / Biso mean: 22.0974 Å2 / Biso min: 3.45 Å2
Refinement stepCycle: final / Resolution: 1.982→41.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 33 150 2248
Biso mean--31.69 28.69 -
Num. residues----257
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.982-2.08640.22251190.1909280399
2.0864-2.21710.24121170.18092838100
2.2171-2.38830.21541520.18322803100
2.3883-2.62860.25471250.1962844100
2.6286-3.00890.21411500.18982847100
3.0089-3.79050.22351730.17312840100
3.7905-41.2260.21011910.1748297399

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