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- PDB-6b9l: Crystal structure of EphA2 with peptide 135E2 -

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Basic information

Entry
Database: PDB / ID: 6b9l
TitleCrystal structure of EphA2 with peptide 135E2
Components
  • Ephrin type-A receptor 2
  • HIS TAG CLEAVED OFF
  • peptide 135E2, (DUG)SAYPDSVPFR
KeywordsTRANSFERASE / complex / ligand binding domain
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 / leading edge membrane ...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 / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / response to growth factor / bone remodeling / positive regulation of bicellular tight junction assembly / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / tight junction / RND1 GTPase cycle / neural tube development / 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 / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / transmembrane receptor protein tyrosine kinase activity / RAC1 GTPase cycle / osteoclast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / molecular function activator activity / protein localization to plasma membrane / skeletal system development / cell chemotaxis / positive regulation of protein localization to plasma membrane / cell motility / 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 / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / neuron differentiation / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / defense response to Gram-positive bacterium / cell adhesion / positive regulation of cell migration / cadherin binding / inflammatory response / focal adhesion / 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) / Galactose-binding domain-like / 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 / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsSong, J. / Tan, X.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structure-Based Design of Novel EphA2 Agonistic Agents with Nanomolar Affinity in Vitro and in Cell.
Authors: Gambini, L. / Salem, A.F. / Udompholkul, P. / Tan, X.F. / Baggio, C. / Shah, N. / Aronson, A. / Song, J. / Pellecchia, M.
History
DepositionOct 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Ephrin type-A receptor 2
C: Ephrin type-A receptor 2
D: Ephrin type-A receptor 2
E: peptide 135E2, (DUG)SAYPDSVPFR
F: peptide 135E2, (DUG)SAYPDSVPFR
G: peptide 135E2, (DUG)SAYPDSVPFR
H: peptide 135E2, (DUG)SAYPDSVPFR
J: HIS TAG CLEAVED OFF


Theoretical massNumber of molelcules
Total (without water)94,9859
Polymers94,9859
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.268, 94.153, 134.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 22242.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK
Production host: Escherichia coli O103:H2 str. 12009 (bacteria)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein/peptide
peptide 135E2, (DUG)SAYPDSVPFR


Mass: 1325.806 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli K-12 (bacteria)
#3: Protein/peptide HIS TAG CLEAVED OFF


Mass: 712.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli O103:H2 str. 12009 (bacteria)
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: 2.98 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Lithium sulphate, Tris-Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 18465 / % possible obs: 96 % / Redundancy: 3.5 % / Net I/σ(I): 3.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 3.2→47.08 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 1848 10.03 %
Rwork0.235 --
obs0.239 18426 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5954 0 0 0 5954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016130
X-RAY DIFFRACTIONf_angle_d1.0558304
X-RAY DIFFRACTIONf_dihedral_angle_d20.1892188
X-RAY DIFFRACTIONf_chiral_restr0.044875
X-RAY DIFFRACTIONf_plane_restr0.0031063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.202-3.28850.35471430.32951189X-RAY DIFFRACTION92
3.2885-3.38530.32421270.3041271X-RAY DIFFRACTION97
3.3853-3.49450.32991600.28021278X-RAY DIFFRACTION98
3.4945-3.61940.30851370.25221283X-RAY DIFFRACTION97
3.6194-3.76420.31161420.25861263X-RAY DIFFRACTION97
3.7642-3.93540.29581420.25661286X-RAY DIFFRACTION97
3.9354-4.14280.31251340.23511256X-RAY DIFFRACTION96
4.1428-4.40220.25361400.2221256X-RAY DIFFRACTION95
4.4022-4.74180.22211450.20111286X-RAY DIFFRACTION96
4.7418-5.21840.23441360.19241295X-RAY DIFFRACTION96
5.2184-5.97230.24641450.2111272X-RAY DIFFRACTION95
5.9723-7.51950.26771460.22661294X-RAY DIFFRACTION95
7.5195-47.08160.23851510.21691349X-RAY DIFFRACTION94

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