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- PDB-5neg: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-13]-OEt -

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Basic information

Entry
Database: PDB / ID: 5neg
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-13]-OEt
ComponentsProtein enabled homolog
KeywordsCELL ADHESION / proline-rich motif / Ena/VASP inhibitor / actin / protein-protein interaction
Function / homology
Function and homology information


actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / WW domain binding / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / cell junction ...actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / WW domain binding / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / cell junction / lamellipodium / actin binding / cytoskeleton / focal adhesion / synapse / plasma membrane / cytosol
Similarity search - Function
VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-8VK / NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsBarone, M. / Roske, Y.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells.
Authors: Barone, M. / Muller, M. / Chiha, S. / Ren, J. / Albat, D. / Soicke, A. / Dohmen, S. / Klein, M. / Bruns, J. / van Dinther, M. / Opitz, R. / Lindemann, P. / Beerbaum, M. / Motzny, K. / Roske, ...Authors: Barone, M. / Muller, M. / Chiha, S. / Ren, J. / Albat, D. / Soicke, A. / Dohmen, S. / Klein, M. / Bruns, J. / van Dinther, M. / Opitz, R. / Lindemann, P. / Beerbaum, M. / Motzny, K. / Roske, Y. / Schmieder, P. / Volkmer, R. / Nazare, M. / Heinemann, U. / Oschkinat, H. / Ten Dijke, P. / Schmalz, H.G. / Kuhne, R.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions.
Authors: Opitz, R. / Mueller, M. / Reuter, C. / Barone, M. / Soicke, A. / Roske, Y. / Piotukh, K. / Huy, P. / Beerbaum, M. / Wiesner, B. / Beyermann, M. / Schmieder, P. / Freund, C. / Volkmer, R. / ...Authors: Opitz, R. / Mueller, M. / Reuter, C. / Barone, M. / Soicke, A. / Roske, Y. / Piotukh, K. / Huy, P. / Beerbaum, M. / Wiesner, B. / Beyermann, M. / Schmieder, P. / Freund, C. / Volkmer, R. / Oschkinat, H. / Schmalz, H.G. / Kuehne, R.
History
DepositionMar 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Nov 25, 2020Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein enabled homolog
B: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,25512
Polymers25,2572
Non-polymers1,99910
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-9 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.810, 44.360, 72.470
Angle α, β, γ (deg.)90.00, 96.56, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Protein enabled homolog


Mass: 12628.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENAH, MENA / Plasmid: pGEX-4T-1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8N8S7
#2: Chemical ChemComp-8VK / ethyl (3~{S},7~{R},10~{R},11~{R},13~{S})-4-[(3~{S},6~{R},8~{a}~{S})-1'-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8~{a}-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-11-ethyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylate


Mass: 734.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H48ClN5O7
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M ammonium sulfate, 260mM ammonium nitrate / Temp details: plate hotel

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.29→44.3862 Å / Num. obs: 53114 / % possible obs: 95.9 % / Redundancy: 4.7 % / CC1/2: 0.994 / Rrim(I) all: 0.156 / Net I/σ(I): 6.76
Reflection shellResolution: 1.29→1.39 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 9979 / CC1/2: 0.656 / Rrim(I) all: 0.764 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NCG

5ncg


Resolution: 1.29→44.36 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 2656 5 %
Rwork0.1532 --
obs0.1551 53116 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.29→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 137 249 2112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082049
X-RAY DIFFRACTIONf_angle_d1.2082800
X-RAY DIFFRACTIONf_dihedral_angle_d14.705927
X-RAY DIFFRACTIONf_chiral_restr0.083290
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.31350.31991310.29032486X-RAY DIFFRACTION92
1.3135-1.33870.30191310.25672483X-RAY DIFFRACTION89
1.3387-1.36610.30521310.23282484X-RAY DIFFRACTION92
1.3661-1.39580.29851320.22242516X-RAY DIFFRACTION89
1.3958-1.42820.26991280.19952430X-RAY DIFFRACTION90
1.4282-1.46390.24171280.18612425X-RAY DIFFRACTION88
1.4639-1.50350.2251340.17962544X-RAY DIFFRACTION91
1.5035-1.54780.23351400.16472674X-RAY DIFFRACTION97
1.5478-1.59770.22661440.16282734X-RAY DIFFRACTION99
1.5977-1.65480.21041460.15292762X-RAY DIFFRACTION99
1.6548-1.72110.20341440.16192740X-RAY DIFFRACTION99
1.7211-1.79940.17721440.13292743X-RAY DIFFRACTION100
1.7994-1.89430.18441460.13392764X-RAY DIFFRACTION100
1.8943-2.0130.17521450.12772784X-RAY DIFFRACTION100
2.013-2.16840.18511450.13052753X-RAY DIFFRACTION99
2.1684-2.38660.17281450.14232748X-RAY DIFFRACTION100
2.3866-2.73190.18181460.14832773X-RAY DIFFRACTION99
2.7319-3.44170.19721460.14882774X-RAY DIFFRACTION99
3.4417-44.38620.15441500.15132843X-RAY DIFFRACTION99

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