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- PDB-6nkp: EphA2 LBD in complex with bA-WLA-YSKbio peptide -

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Basic information

Entry
Database: PDB / ID: 6nkp
TitleEphA2 LBD in complex with bA-WLA-YSKbio peptide
Components
  • Ephrin type-A receptor 2
  • bA-WLA-YSKbio peptide
KeywordsTRANSFERASE / protein-peptide interaction / kinase / ephrin / eph receptor / drug development / SIGNALING PROTEIN
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 / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...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 / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / negative regulation of chemokine production / ephrin receptor activity / leading edge membrane / bone remodeling / post-anal tail morphogenesis / response to growth factor / activation of GTPase activity / regulation of lamellipodium assembly / tight junction / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell chemotaxis / negative regulation of angiogenesis / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / skeletal system development / cell motility / molecular function activator activity / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / virus receptor activity / lamellipodium / receptor complex / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / cadherin binding / inflammatory response / phosphorylation / 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. / Eph receptor ligand-binding domain profile. ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
BIOTIN / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.033 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 7, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-YSKbio peptide
D: bA-WLA-YSKbio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9185
Polymers45,6744
Non-polymers2441
Water4,972276
1
A: Ephrin type-A receptor 2
C: bA-WLA-YSKbio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0813
Polymers22,8372
Non-polymers2441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13 kcal/mol
Surface area9760 Å2
MethodPISA
2
B: Ephrin type-A receptor 2
C: bA-WLA-YSKbio peptide
D: bA-WLA-YSKbio peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5794
Polymers24,3343
Non-polymers2441
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-14 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.916, 67.094, 93.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+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-YSKbio peptide


Mass: 1497.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Biotin linked to Lys 13 side-chain / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BTN / BIOTIN / Biotin


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.09 M BIS-TRIS pH 5.5, 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: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→29.39 Å / Num. obs: 24912 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.997 / Χ2: 1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.03→2.09 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1673 / CC1/2: 0.714 / Χ2: 0.95 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX(1.14rc2_3191: ???)refinement
XDSJan 26, 2018data reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
PHASER2.8.2phasing
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HEI

3hei


Resolution: 2.033→28.949 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.5
RfactorNum. reflection% reflection
Rfree0.2132 1204 4.84 %
Rwork0.1675 --
obs0.1697 24868 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.033→28.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 15 276 3323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123174
X-RAY DIFFRACTIONf_angle_d1.1714312
X-RAY DIFFRACTIONf_dihedral_angle_d11.5371859
X-RAY DIFFRACTIONf_chiral_restr0.067450
X-RAY DIFFRACTIONf_plane_restr0.008551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.033-2.11440.31561250.23842442X-RAY DIFFRACTION93
2.1144-2.21060.22611280.20062596X-RAY DIFFRACTION99
2.2106-2.32710.20621390.18052594X-RAY DIFFRACTION99
2.3271-2.47280.22871340.18452584X-RAY DIFFRACTION99
2.4728-2.66360.24671410.18092627X-RAY DIFFRACTION99
2.6636-2.93150.23581300.18292635X-RAY DIFFRACTION100
2.9315-3.35510.20911410.15882665X-RAY DIFFRACTION100
3.3551-4.2250.19141340.13382692X-RAY DIFFRACTION100
4.225-28.95150.18181320.15682829X-RAY DIFFRACTION100
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)
15.10063.8895-3.98023.4982-2.74433.26580.0362-0.20080.0143-0.0672-0.1919-0.0160.09820.25320.1810.10950.0261-0.00020.17270.00690.1427-23.4699-12.192937.1397
23.08912.59470.63694.30232.04931.52230.13890.03220.31310.1312-0.03540.1275-0.6346-0.03640.03690.30230.0186-0.02520.159-0.00390.1707-24.59476.445436.0288
38.7777-0.0296-2.77186.78942.09652.2616-0.1516-0.8632-0.3280.60030.3261-0.12090.80220.3794-0.04970.31080.0527-0.00510.3310.06310.279-7.0489-29.957313.8701
45.58510.25040.84315.7226-0.54787.15320.09010.50530.1331-0.80830.06170.44740.4439-0.5092-0.18580.21770.0004-0.05390.2251-0.00450.2163-41.2498-15.82331.6328
54.8662-0.09691.08127.06310.17933.2418-0.09260.1819-0.06150.51650.2332-0.5522-0.12020.46320.03670.13840.0092-0.02430.2644-0.07690.1674-4.5061-9.627717.4631
64.42330.11371.0064.3134-0.13144.4893-0.03660.0392-0.50850.20550.04950.07830.520.0444-0.00690.2037-0.02090.02870.14510.00770.1707-12.7202-23.986613.023
71.5586-0.9666-0.54351.4898-0.42352.21520.10110.0415-0.0391-0.3707-0.0659-0.0495-0.2793-0.11160.00520.1308-0.01960.00010.150.00710.1716-11.5988-13.79455.7815
82.50190.71410.19917.82241.47560.29010.14310.43370.0559-0.283-0.27870.7431-0.5915-0.75320.03460.22590.06660.0190.3790.0170.2004-23.9147-6.688518.4879
95.0735-5.46930.51837.73190.02112.0015-0.0971-0.08970.0251-0.12320.1504-0.20550.01560.136-0.00110.1461-0.06380.02440.1244-0.00230.165-7.2007-21.28412.6665
101.8679-0.3414-0.5254.3651-0.17481.64920.0203-0.01980.1635-0.21210.0916-0.2135-0.2478-0.0402-0.10120.1912-0.02190.01140.15830.00270.1112-10.0026-8.14478.3625
116.6876-0.80930.38733.6634-3.26963.2334-0.11720.11120.115-0.40470.23870.7024-0.2535-0.44120.01330.20650.0403-0.05160.21780.08130.1401-27.9756-0.089728.5819
125.87390.94860.47313.628-0.02716.1588-0.06030.30680.0285-0.33780.09570.3330.0155-0.43760.04110.2047-0.057-0.03260.1708-0.00330.1509-35.278-13.490129.2921
132.45811.3144-0.97861.7268-0.52621.783-0.0377-0.0593-0.02470.0056-0.01380.0843-0.0180.03470.05210.10420.026-0.01310.1466-0.00240.1327-26.0467-11.207439.4268
141.33412.5281-1.01168.5528-1.17563.29480.055-0.9835-0.03040.3826-0.3135-0.62710.25910.01980.26590.16180.0672-0.03890.4138-0.01510.2244-12.4332-12.080826.8021
155.51943.4552-0.33494.7455-2.43861.94470.0330.1785-0.44380.0263-0.1569-0.3930.21420.62210.15740.1310.0637-0.03420.2853-0.0180.1524-17.619-11.363941.2117
166.24763.0872-1.70362.3696-0.95371.45030.1914-0.13940.20010.1056-0.10450.2184-0.07520.0159-0.05540.16540.0464-0.00620.1338-0.01990.2325-33.5351-6.173942.6643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 177 through 188 )
2X-RAY DIFFRACTION2chain 'B' and (resid 189 through 204 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 12 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 12 )
5X-RAY DIFFRACTION5chain 'A' and (resid 26 through 43 )
6X-RAY DIFFRACTION6chain 'A' and (resid 44 through 82 )
7X-RAY DIFFRACTION7chain 'A' and (resid 83 through 126 )
8X-RAY DIFFRACTION8chain 'A' and (resid 127 through 135 )
9X-RAY DIFFRACTION9chain 'A' and (resid 136 through 163 )
10X-RAY DIFFRACTION10chain 'A' and (resid 164 through 200 )
11X-RAY DIFFRACTION11chain 'B' and (resid 26 through 43 )
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 69 )
13X-RAY DIFFRACTION13chain 'B' and (resid 70 through 126 )
14X-RAY DIFFRACTION14chain 'B' and (resid 127 through 135 )
15X-RAY DIFFRACTION15chain 'B' and (resid 136 through 146 )
16X-RAY DIFFRACTION16chain 'B' and (resid 147 through 176 )

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