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- PDB-5n9p: ENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-1]-NH2 -

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Basic information

Entry
Database: PDB / ID: 5n9p
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-1]-NH2
Components
  • Ac-[2-Cl-F]-PP-[ProM-1]-NH2
  • Protein enabled homolog
KeywordsPROTEIN BINDING / 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 / GABA-ergic synapse / filopodium ...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 / GABA-ergic synapse / filopodium / 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
Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.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
B: Protein enabled homolog
A: Protein enabled homolog
C: Ac-[2-Cl-F]-PP-[ProM-1]-NH2
D: Ac-[2-Cl-F]-PP-[ProM-1]-NH2
E: Ac-[2-Cl-F]-PP-[ProM-1]-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2006
Polymers27,1655
Non-polymers351
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: Tetramerization of Ena/VASP is mediated by EVH2 domain (Bachmann1999)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-15 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.266, 47.266, 202.722
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein enabled homolog / ENAH EVH1


Mass: 12628.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Only the backbone of S2B was modelled as side chain was not visible
Source: (gene. exp.) Homo sapiens (human) / Gene: ENAH, MENA / Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q8N8S7
#2: Protein/peptide Ac-[2-Cl-F]-PP-[ProM-1]-NH2


Mass: 636.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.6M ammonium sulfate, 500mM lithium chloride / Temp details: Plate hotel

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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 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.8→41 Å / Num. obs: 25337 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4010 / CC1/2: 0.581 / % possible all: 99.7

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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: 1.8→40.124 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1266 5 %Random
Rwork0.2026 ---
obs0.2038 25336 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 139 65 1925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081969
X-RAY DIFFRACTIONf_angle_d1.2732687
X-RAY DIFFRACTIONf_dihedral_angle_d11.221361
X-RAY DIFFRACTIONf_chiral_restr0.061279
X-RAY DIFFRACTIONf_plane_restr0.007350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7998-1.87180.30081380.28912627X-RAY DIFFRACTION100
1.8718-1.9570.25061380.24532622X-RAY DIFFRACTION100
1.957-2.06020.25921390.22332650X-RAY DIFFRACTION100
2.0602-2.18930.24411380.20982621X-RAY DIFFRACTION100
2.1893-2.35830.22911400.18782656X-RAY DIFFRACTION100
2.3583-2.59560.26251400.20622658X-RAY DIFFRACTION100
2.5956-2.97110.26411410.21432687X-RAY DIFFRACTION100
2.9711-3.74280.21781430.20632707X-RAY DIFFRACTION99
3.7428-40.13370.19011490.17962842X-RAY DIFFRACTION98
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)
11.90990.08380.62181.85230.28691.01710.03120.21650.0299-0.0602-0.015-0.06080.00730.01840.00310.1773-0.00580.02270.2316-0.01650.22114.443452.3838230.7101
20.5846-0.40930.44461.3652-0.45921.11340.65130.1456-0.5982-0.3942-0.0524-0.2361.451-0.07010.36530.9199-0.0214-0.22530.353-0.00890.4455-9.640342.0842209.8142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 1 through 111)
2X-RAY DIFFRACTION2(chain 'A' and resid 5 through 111)

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