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- PDB-6nk2: EphA2 LBD in complex with bA-WLA-YRPK bio peptide -

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Basic information

Entry
Database: PDB / ID: 6nk2
TitleEphA2 LBD in complex with bA-WLA-YRPK bio peptide
Components
  • Ephrin type-A receptor 2
  • bA-WLA-YPRKbio peptide
KeywordsTRANSFERASE / protein-peptide interaction / kinase / ephrin / eph receptor / drug development / SIGNALING PROTEIN
Function / homology
Function and homology information


notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity ...notochord cell development / notochord formation / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / lens fiber cell morphogenesis / axial mesoderm formation / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / response to growth factor / post-anal tail morphogenesis / activation of GTPase activity / bone remodeling / positive regulation of bicellular tight junction assembly / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / tight junction / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / RHOV GTPase cycle / growth factor binding / EPHA-mediated growth cone collapse / regulation of cell adhesion mediated by integrin / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / vasculogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / molecular function activator activity / negative regulation of angiogenesis / skeletal system development / cell chemotaxis / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / osteoblast differentiation / cell migration / lamellipodium / virus receptor activity / angiogenesis / receptor complex / cell adhesion / defense response to Gram-positive bacterium / 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 / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / 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
DI(HYDROXYETHYL)ETHER / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLechtenberg, B.C. / Pasquale, E.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS087070 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA030199 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Engineering nanomolar peptide ligands that differentially modulate EphA2 receptor signaling.
Authors: Gomez-Soler, M. / Petersen Gehring, M. / Lechtenberg, B.C. / Zapata-Mercado, E. / Hristova, K. / Pasquale, E.B.
History
DepositionJan 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 16, 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: bA-WLA-YPRKbio peptide
D: bA-WLA-YPRKbio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1145
Polymers46,0084
Non-polymers1061
Water2,882160
1
A: Ephrin type-A receptor 2
C: bA-WLA-YPRKbio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1103
Polymers23,0042
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-8 kcal/mol
Surface area9870 Å2
MethodPISA
2
B: Ephrin type-A receptor 2
D: bA-WLA-YPRKbio peptide


Theoretical massNumber of molelcules
Total (without water)23,0042
Polymers23,0042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-13 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.441, 155.441, 51.906
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYVALVAL(chain 'A' and (resid 25 through 72 or resid 74 through 201))AA25 - 725 - 52
121SERSERLYSLYS(chain 'A' and (resid 25 through 72 or resid 74 through 201))AA74 - 20054 - 180
231GLYGLYVALVAL(chain 'B' and (resid 25 through 72 or resid 74 through 201))BB25 - 725 - 52
241SERSERLYSLYS(chain 'B' and (resid 25 through 72 or resid 74 through 201))BB74 - 20054 - 180
152TRPTRPLYSLYS(chain 'C' and resid 2 through 14)CC2 - 142 - 14
262TRPTRPLYSLYSchain 'D'DD2 - 142 - 14

NCS ensembles :
ID
1
2

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Components

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


Mass: 21339.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Production host: Escherichia coli (E. coli)
References: UniProt: P29317, receptor protein-tyrosine kinase
#2: Protein/peptide bA-WLA-YPRKbio peptide


Mass: 1664.900 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Biotin is linked to the of side-chain of LysB14. Biotin is not observed in the model
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 4.15 Å3/Da / Density % sol: 70.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.09 M Sodium-Acetate pH 4.5, 22.5% w/v PEG 3,350, 3% w/v 6-aminohexanoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→29.38 Å / Num. obs: 36732 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 35.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.05 / Rrim(I) all: 0.164 / Χ2: 0.98 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.438 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3157 / CC1/2: 0.527 / Rpim(I) all: 0.522 / Rrim(I) all: 1.532 / Χ2: 0.91 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14rc2-3191refinement
XDSJan 26, 2018data reduction
Aimless0.6.2data scaling
PHASER2.8.2phasing
Coot0.8.9.1model building
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HEI

3hei


Resolution: 2.2→29.38 Å / SU ML: 0.2328 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4284
RfactorNum. reflection% reflection
Rfree0.2092 1882 5.13 %
Rwork0.1882 --
obs0.1894 36706 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 7 160 3241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323175
X-RAY DIFFRACTIONf_angle_d0.71194306
X-RAY DIFFRACTIONf_chiral_restr0.0477447
X-RAY DIFFRACTIONf_plane_restr0.0038554
X-RAY DIFFRACTIONf_dihedral_angle_d11.26581869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.30561320.26922667X-RAY DIFFRACTION100
2.26-2.330.27881440.24752642X-RAY DIFFRACTION100
2.33-2.40.25751250.23392678X-RAY DIFFRACTION100
2.4-2.490.26261100.2242700X-RAY DIFFRACTION100
2.49-2.590.24871530.21852670X-RAY DIFFRACTION100
2.59-2.70.25751440.21482637X-RAY DIFFRACTION100
2.7-2.850.25481300.2092672X-RAY DIFFRACTION100
2.85-3.020.26061440.22332689X-RAY DIFFRACTION100
3.02-3.260.21011510.19392667X-RAY DIFFRACTION100
3.26-3.590.19131310.182684X-RAY DIFFRACTION100
3.59-4.10.1971660.16862679X-RAY DIFFRACTION100
4.1-5.160.16241670.13972691X-RAY DIFFRACTION99.97
5.16-29.380.18511850.17872748X-RAY DIFFRACTION99.9
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)
14.860254878571.64475419172-1.822076127747.48299190028-2.56644953465.6179817927-0.1451208353870.04189993922940.4216954077880.399022210489-0.22113920934-0.429421821181-0.4865069190660.1609699940640.3177139580760.375850349735-0.0106258026412-0.06302126816030.196735511593-0.02442728250340.268271759516-66.09884036120.82937931222.08875474606
27.80838937397-0.1044780222330.3747016824832.76230628763-3.176315526723.666757626880.109302249801-0.429802806383-0.08172994958321.28730269068-0.6093276785190.1343101948240.6988737308120.3364139885790.2297739040140.7965725064440.06125922934880.06021800655660.4590728861610.04613680367650.325909813702-99.546981612532.349066233313.9553088089
37.693351544292.923213632643.629322667352.53989205958-1.283326789887.94829231365-0.4164577704020.4458802189220.0626929145894-0.3277733069280.1800762143270.1906472716030.2488180277840.392977307084-0.05925256858240.3826346244970.05682970586980.05353926705780.2039976606780.06830957431490.295245834041-78.417441275917.3337035928-12.8291975516
46.590468822042.143527508671.368014345856.16275117871-1.448577113645.955468649710.0331823780391-0.102628044140.07888705628550.0112243861942-0.414065824989-0.277667001634-0.3950598998920.4553058808130.4017546256950.3972114466970.0051078820396-0.0223792082590.1673296903050.003166201170910.258833191877-70.255606982419.23194192020.260999305685
54.052526160070.7079337938611.699620738633.948251319792.173216480993.02643502171-0.250411201577-0.2328814485280.152815951457-0.0762762780815-0.06692632949130.191329760778-0.508943939717-0.1303815113450.2760251946320.2976396715990.01150959852320.09233278729750.203022126224-0.006518681312720.217913092985-82.964160815412.2973606684-0.0215198130137
64.561584983020.5138431719023.250578299821.661112322960.3550027290353.33317909447-0.05764167507510.151865050695-0.134838167391-0.01620080762370.0307623153881-0.207297477229-0.04810340627650.308606928426-0.1025896248650.3714831296350.01548949163660.08552130997020.2192020775850.01844121840270.305208383964-71.52316776145.50529905313-2.66980186256
74.813278619563.12991060808-4.728211700722.11695543545-3.053765857814.731218927380.161890667232-0.942528824241-0.03185777273811.280682422840.02445483233470.00199498728098-0.1884755605970.284644007864-0.0848186775680.5656374399820.06732089920180.005292504894760.3582756343820.05324407937590.375046744258-68.07968141092.9769502487413.007579965
80.789299182571.009946168720.1875751593815.093426104951.356596371593.30381835863-0.0549233896101-0.1531591495560.0521901428595-0.173452394878-0.3359119981450.955703130384-0.348454440865-0.6756849180620.4257251143420.3836878055870.05288164505060.04208940911590.355412250388-0.09990286537560.387931447073-89.583844070613.1932319202-0.424813302203
92.28594006060.2275266534111.916070991132.82728441338-0.5635922443532.227105909410.124527801956-0.305398868018-0.4220787394680.00491961735832-0.1803646722-0.2330420197040.1928447829520.129774514290.08389303422320.3571275927210.004360731830160.07100773881590.223416056443-0.01547892393410.275616092177-70.71513751045.34042921007-0.0768689104092
106.198462395041.759779060154.118751697621.359338276390.09990157893784.484929858-0.0649867431321-0.139487247467-0.744670098762-0.1054366948050.005587271905490.2139223318150.0379784379636-0.278133753620.03980760832670.40694537182-0.009887994226820.01610588718140.16928830541-0.03549632061660.28993125865-86.21416004435.99026965161-10.0398805084
116.824621477810.5904416553115.13893616512.484162638750.2145549110875.38336304453-0.044803125696-0.3214870351670.0550468329766-0.0571900144681-0.159240098760.2094247545580.0666824154991-0.4223859129960.1211503900490.3113705060530.02421386061920.07457606120470.202565534336-0.02036112293340.290882386762-81.700916626610.3267812170.844227676158
123.47526268740.8782209069373.366396269833.349554085820.4481483439865.85967738553-0.3277119046630.71951293903-0.322820593494-0.5424418539210.324814696972-0.110267630062-0.09939752170250.844349991208-0.05635759912020.396911011519-0.07222507664020.03973561922380.208050998452-0.03087028275760.29037296276-79.596807242310.5528447068-13.5978573977
132.35092114918-3.20711187992-3.029355334479.684658715720.5466818312117.61387850834-0.4978728896140.493764281079-0.982441233206-0.2129281741080.37411797111.334905014810.311870923257-1.647225028910.179712057880.391038158779-0.116942474610.05007949739860.664716130921-0.04511217656510.530864182159-106.35383345131.4223040557-12.4214051476
144.07904014622.00267758245-1.630337004377.641501133570.9348731512622.457549934320.0574676120043-0.300296924915-0.2728095627511.09938463269-0.317779230914-0.09760040500290.5528120524370.4592461108290.01093434859910.5152892003690.116316250085-0.001582266019250.2906280693160.04602062533480.327549195034-92.492149942731.00745461834.65181349729
157.564586868973.438432192410.9118323034672.327675437810.03487057503948.55136545081-0.21361091141-0.53115470426-0.3329665324370.516291646648-0.08339675315420.7052333215241.12822305571-0.5950345352920.1420765730920.5546643268220.04395725809480.1962471824140.3357052632020.01581378817710.441332932929-103.68126124131.1832341779.92963465772
162.32587115642-0.45554633069-0.6250979836852.493931374750.6305116194543.27680852773-0.120881087667-0.141858586540.02934638208980.0840484125057-0.0529036545246-0.000922149952531-0.05683187848240.03721207140280.1671443950110.2882631692790.0722653028768-0.01060492618070.2358064848360.02935313364310.268092816247-94.199284645841.0113302261-1.1794615763
174.181083658610.560380970443-1.026638470016.576874631973.496275245282.62496153377-0.1965687160570.469558948702-0.0694509486941-0.1003999332830.02873590827020.5429983939820.0598973349433-0.04584557360550.3684983669920.3018497019480.05687422341940.0227102118520.2388441372750.005871486424220.32493422445-102.35277031934.5279086515-8.79467999383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 2 through 14 )
2X-RAY DIFFRACTION2chain 'D' and (resid 2 through 14 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 43 )
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 93 )
6X-RAY DIFFRACTION6chain 'A' and (resid 94 through 107 )
7X-RAY DIFFRACTION7chain 'A' and (resid 108 through 117 )
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 135 )
9X-RAY DIFFRACTION9chain 'A' and (resid 136 through 163 )
10X-RAY DIFFRACTION10chain 'A' and (resid 164 through 176 )
11X-RAY DIFFRACTION11chain 'A' and (resid 177 through 188 )
12X-RAY DIFFRACTION12chain 'A' and (resid 189 through 201 )
13X-RAY DIFFRACTION13chain 'B' and (resid 23 through 33 )
14X-RAY DIFFRACTION14chain 'B' and (resid 34 through 52 )
15X-RAY DIFFRACTION15chain 'B' and (resid 53 through 69 )
16X-RAY DIFFRACTION16chain 'B' and (resid 70 through 188 )
17X-RAY DIFFRACTION17chain 'B' and (resid 189 through 201 )

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