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- PDB-5n9c: ENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-1]-OH -

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Basic information

Entry
Database: PDB / ID: 5n9c
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-1]-OH
Components
  • Ac-[2-Cl-F]-PP-[ProM-1]-OH
  • Protein 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
NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsBarone, M. / Roske, Y.
CitationJournal: 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.
History
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: 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.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: 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
B: Protein enabled homolog
F: Ac-[2-Cl-F]-PP-[ProM-1]-OH
G: Ac-[2-Cl-F]-PP-[ProM-1]-OH
H: Ac-[2-Cl-F]-PP-[ProM-1]-OH
M: Ac-[2-Cl-F]-PP-[ProM-1]-OH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,46814
Polymers27,8096
Non-polymers6588
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-48 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.761, 43.386, 43.593
Angle α, β, γ (deg.)61.40, 84.03, 84.10
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABFGHM

#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 (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8N8S7
#2: Protein/peptide
Ac-[2-Cl-F]-PP-[ProM-1]-OH


Mass: 638.153 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 251 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.25 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M ammonium sulfate, 200mM potassium nitrate / Temp details: plate hotel

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.16→38.2 Å / Num. obs: 71797 / % possible obs: 93.1 % / Redundancy: 2 % / CC1/2: 0.999 / Rrim(I) all: 0.048 / Net I/σ(I): 11.24
Reflection shellResolution: 1.16→1.23 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.86 / Num. unique obs: 12432 / CC1/2: 0.826 / Rrim(I) all: 0.517 / % possible all: 90

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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: 5N91

5n91


Resolution: 1.16→37.122 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.04
RfactorNum. reflection% reflection
Rfree0.1691 3590 5 %
Rwork0.1385 --
obs0.1401 71779 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.16→37.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 223 243 2222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132247
X-RAY DIFFRACTIONf_angle_d1.7013082
X-RAY DIFFRACTIONf_dihedral_angle_d16.3881128
X-RAY DIFFRACTIONf_chiral_restr0.1311
X-RAY DIFFRACTIONf_plane_restr0.011410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.17530.27121340.2662545X-RAY DIFFRACTION90
1.1753-1.19140.30261310.24652503X-RAY DIFFRACTION90
1.1914-1.20840.25691350.23342565X-RAY DIFFRACTION90
1.2084-1.22640.24041330.21882522X-RAY DIFFRACTION91
1.2264-1.24560.2431360.22262585X-RAY DIFFRACTION91
1.2456-1.2660.26441330.2062526X-RAY DIFFRACTION91
1.266-1.28780.25081390.20332622X-RAY DIFFRACTION92
1.2878-1.31130.25451340.19242562X-RAY DIFFRACTION92
1.3113-1.33650.22051360.18382573X-RAY DIFFRACTION92
1.3365-1.36380.221360.17742587X-RAY DIFFRACTION92
1.3638-1.39340.19391390.15562637X-RAY DIFFRACTION93
1.3934-1.42580.18281360.15012588X-RAY DIFFRACTION93
1.4258-1.46150.16371370.13752595X-RAY DIFFRACTION93
1.4615-1.5010.14741400.12842659X-RAY DIFFRACTION93
1.501-1.54520.17121370.11992607X-RAY DIFFRACTION94
1.5452-1.59510.14351390.11172650X-RAY DIFFRACTION94
1.5951-1.65210.151400.10772647X-RAY DIFFRACTION94
1.6521-1.71820.15751390.11712654X-RAY DIFFRACTION95
1.7182-1.79640.14491400.11092655X-RAY DIFFRACTION95
1.7964-1.89110.14511420.11362704X-RAY DIFFRACTION95
1.8911-2.00960.14991430.10972706X-RAY DIFFRACTION96
2.0096-2.16470.16011430.11222711X-RAY DIFFRACTION96
2.1647-2.38250.13061400.1162670X-RAY DIFFRACTION96
2.3825-2.72720.14561420.12432701X-RAY DIFFRACTION97
2.7272-3.43560.15311430.1372717X-RAY DIFFRACTION96
3.4356-37.1410.17451430.1442698X-RAY DIFFRACTION97

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