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- PDB-4my6: EnaH-EVH1 in complex with peptidomimetic low-molecular weight inh... -

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Basic information

Entry
Database: PDB / ID: 4my6
TitleEnaH-EVH1 in complex with peptidomimetic low-molecular weight inhibitor Ac-[2-Cl-F]-[ProM-2]-[ProM-1]-OH
ComponentsProtein enabled homolog
KeywordsCell adhesion/inhibitor / MOLECULAR RECOGNITION / ACTIN DYNAMICS / Cell adhesion-inhibitor complex
Function / homology
Function and homology information


actin polymerization-dependent cell motility / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / lamellipodium ...actin polymerization-dependent cell motility / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / lamellipodium / cell junction / 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
(3AR,5AS,8S,10AS)-1-[(3S,6R,8AS)-1'-[(2S)-2-ACETAMIDO-3-(2-CHLOROPHENYL)PROPANOYL]-5-OXIDANYLIDENE-SPIRO[1,2,3,8A-TETRAHYDROINDOLIZINE-6,2'-PYRROLIDINE]-3-YL]CARBONYL-10-OXIDANYLIDENE-2,3,3A,5A,8,10A-HEXAHYDRODIPYRROLO[3,2-B:3',1'-F]AZEPINE-8-CARBOXYLIC ACID / : / BROMIDE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBarone, M. / Roske, Y. / Kuehne, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions.
Authors: Opitz, R. / Muller, 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. / Muller, 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. / Kuhne, R.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3May 6, 2015Group: Database references
Revision 1.4Jul 22, 2015Group: Structure summary
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7696
Polymers25,2572
Non-polymers1,5124
Water2,954164
1
A: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4644
Polymers12,6281
Non-polymers8363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3042
Polymers12,6281
Non-polymers6761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.830, 131.420, 35.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-202-

BR

21B-327-

HOH

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Components

#1: Protein Protein enabled homolog


Mass: 12628.273 Da / Num. of mol.: 2 / Fragment: EVH1 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENAH, MENA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8N8S7
#2: Chemical ChemComp-3VH / (3aR,5aS,8S,10aS)-1-[(3S,6R,8aS)-1'-[(2S)-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8a-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-10-oxidanylidene-2,3,3a,5a,8,10a-hexahydrodipyrrolo[3,2-b:3',1'-f]azepine-8-carboxylic acid


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 676.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H38ClN5O7
References: (3AR,5AS,8S,10AS)-1-[(3S,6R,8AS)-1'-[(2S)-2-ACETAMIDO-3-(2-CHLOROPHENYL)PROPANOYL]-5-OXIDANYLIDENE-SPIRO[1,2,3,8A-TETRAHYDROINDOLIZINE-6,2'-PYRROLIDINE]-3-YL]CARBONYL-10-OXIDANYLIDENE- ...References: (3AR,5AS,8S,10AS)-1-[(3S,6R,8AS)-1'-[(2S)-2-ACETAMIDO-3-(2-CHLOROPHENYL)PROPANOYL]-5-OXIDANYLIDENE-SPIRO[1,2,3,8A-TETRAHYDROINDOLIZINE-6,2'-PYRROLIDINE]-3-YL]CARBONYL-10-OXIDANYLIDENE-2,3,3A,5A,8,10A-HEXAHYDRODIPYRROLO[3,2-B:3',1'-F]AZEPINE-8-CARBOXYLIC ACID
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.2M ammonium sulphate, 200mM ammonium bromide, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2012
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. all: 23715 / Num. obs: 23659 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.074 / Net I/σ(I): 4.02
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.11 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.35 / % possible all: 99.9

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Processing

Software
NameClassification
REFMACrefinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EVH

1evh


Resolution: 1.7→32.064 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.2382 1183 RANDOM
Rwork0.1892 --
all-23715 -
obs-23659 -
Refinement stepCycle: LAST / Resolution: 1.7→32.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 98 164 2014

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