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- PDB-5ndu: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-12]-OMe -

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Basic information

Entry
Database: PDB / ID: 5ndu
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-12]-OMe
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 / WW domain 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 / profilin binding / WW domain 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
methyl / NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 9, 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 / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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

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)27,83011
Polymers25,2572
Non-polymers2,5739
Water2,864159
1
A: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5715
Polymers12,6281
Non-polymers9424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2596
Polymers12,6281
Non-polymers1,6315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.150, 34.570, 44.240
Angle α, β, γ (deg.)90.00, 96.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q8N8S7

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Non-polymers , 5 types, 168 molecules

#2: Chemical ChemComp-8V2 / methyl (3~{S},7~{R},10~{R},13~{R})-4-[(3~{S},6~{R},8~{a}~{S})-1'-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylid ene-spiro[1,2,3,8~{a}-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3, 7}]tridec-8-ene-13-carboxylate / Ac-[2-Cl-F]-[ProM-2]-[ProM-12]-OMe / Methyl group


Mass: 692.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H42ClN5O7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0M ammonium sulfate, 220mM 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: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.42→43.9378 Å / Num. obs: 38981 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rrim(I) all: 0.12 / Net I/σ(I): 11.36
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.25 / Num. unique obs: 5881 / CC1/2: 0.593 / Rrim(I) all: 1.714 / % possible all: 99.9

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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: 1.42→43.917 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 1947 5 %
Rwork0.1714 --
obs0.1729 38952 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→43.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 164 159 2069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172121
X-RAY DIFFRACTIONf_angle_d1.742907
X-RAY DIFFRACTIONf_dihedral_angle_d24.9611031
X-RAY DIFFRACTIONf_chiral_restr0.102300
X-RAY DIFFRACTIONf_plane_restr0.012386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4199-1.45540.40231380.39982613X-RAY DIFFRACTION100
1.4554-1.49480.36961380.32532624X-RAY DIFFRACTION100
1.4948-1.53880.27861380.26812619X-RAY DIFFRACTION100
1.5388-1.58840.29011380.24152629X-RAY DIFFRACTION100
1.5884-1.64520.26621380.2282638X-RAY DIFFRACTION100
1.6452-1.71110.26451390.21682626X-RAY DIFFRACTION100
1.7111-1.7890.21111370.17982604X-RAY DIFFRACTION100
1.789-1.88330.18861370.16532615X-RAY DIFFRACTION100
1.8833-2.00130.20051410.15452673X-RAY DIFFRACTION100
2.0013-2.15580.18361390.14372634X-RAY DIFFRACTION100
2.1558-2.37270.1631390.14362639X-RAY DIFFRACTION100
2.3727-2.7160.21251390.15012657X-RAY DIFFRACTION100
2.716-3.42170.17081420.14762691X-RAY DIFFRACTION100
3.4217-43.93780.16451440.15552743X-RAY DIFFRACTION100
Refinement TLS params.

T23: -0.0035 Å2 / 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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.251-0.0467-0.68342.38960.30922.13720.00820.05630.0235-0.1188-0.01470.1914-0.0571-0.060.00760.13560.0021-0.00060.09040.0972-16.743-28.6646-2.5892
21.0418-0.00260.65822.55190.3543.28120.0092-0.0195-0.0252-0.1454-0.01080.1649-0.1136-0.0990.00890.21320.00910.02860.11190.1178-19.0315-10.931620.4394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 0 through 111)
2X-RAY DIFFRACTION2(chain 'A' and resid 3 through 111)

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