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- PDB-5nbf: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-3]-OH -

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Basic information

Entry
Database: PDB / ID: 5nbf
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-3]-OH
ComponentsProtein enabled homolog
KeywordsCELL ADHESION / proline-rich motif / Ena/VASP inhibitor / actin / protein-protein interaction
Function / homology
Function and homology information


postsynaptic cytoskeleton organization / actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / WW domain binding / Generation of second messenger molecules / axon guidance / filopodium / GABA-ergic synapse ...postsynaptic cytoskeleton organization / actin polymerization-dependent cell motility / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / WW domain binding / Generation of second messenger molecules / axon guidance / filopodium / GABA-ergic synapse / SH3 domain binding / lamellipodium / actin binding / cytoskeleton / postsynapse / focal adhesion / 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-8S8 / NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4534
Polymers12,6281
Non-polymers8243
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Tetramerization of Ena/VASP is mediated by EVH2 domain (Bachmann1999)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-13 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.607, 38.251, 44.002
Angle α, β, γ (deg.)90.00, 90.59, 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.: 1
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 (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8N8S7
#2: Chemical ChemComp-8S8 / (3~{S},6~{S},7~{R},9~{a}~{R})-6-[[(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]carbonylamino]-7-methyl-5-oxidanylidene-1,2,3,6,7,9~{a}-hexahydropyrrolo[1,2-a]azepine-3-carboxylic acid


Mass: 666.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H40ClN5O7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1M ammonium sulfate, 180mM ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.15→44 Å / Num. obs: 38436 / % possible obs: 93.5 % / Redundancy: 2.2 % / CC1/2: 0.999 / Rrim(I) all: 0.045 / Net I/σ(I): 13.15
Reflection shellResolution: 1.15→1.22 Å / Redundancy: 2.1 % / Num. unique all: 6060 / Num. unique obs: 6060 / CC1/2: 0.591 / Rrim(I) all: 0.782 / % possible all: 92

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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: 5N9C

5n9c


Resolution: 1.15→25.662 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.53
RfactorNum. reflection% reflection
Rfree0.1615 1922 5 %
Rwork0.1368 --
obs0.1381 38424 93.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.15→25.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 0 56 140 1065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131093
X-RAY DIFFRACTIONf_angle_d1.411503
X-RAY DIFFRACTIONf_dihedral_angle_d21.883492
X-RAY DIFFRACTIONf_chiral_restr0.096155
X-RAY DIFFRACTIONf_plane_restr0.011204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.149-1.17770.33161300.30812478X-RAY DIFFRACTION91
1.1777-1.20950.28331360.25452583X-RAY DIFFRACTION93
1.2095-1.24510.25571360.23062577X-RAY DIFFRACTION93
1.2451-1.28530.26531360.20662588X-RAY DIFFRACTION93
1.2853-1.33120.22531380.17772615X-RAY DIFFRACTION94
1.3312-1.38450.20491380.15862621X-RAY DIFFRACTION95
1.3845-1.44750.19931390.14482647X-RAY DIFFRACTION96
1.4475-1.52390.15251420.11292692X-RAY DIFFRACTION96
1.5239-1.61930.15191400.10372666X-RAY DIFFRACTION96
1.6193-1.74430.14871400.10572643X-RAY DIFFRACTION95
1.7443-1.91980.15281340.10742560X-RAY DIFFRACTION91
1.9198-2.19750.12391350.10792559X-RAY DIFFRACTION91
2.1975-2.76810.13741340.12832556X-RAY DIFFRACTION91
2.7681-25.66830.14861440.13972717X-RAY DIFFRACTION94

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