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- PDB-5ncf: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-4]-OH -

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Basic information

Entry
Database: PDB / ID: 5ncf
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-4]-OH
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 / WW domain binding / profilin binding / Signaling by ROBO receptors / actin polymerization or depolymerization / Generation of second messenger molecules / filopodium / axon guidance / SH3 domain binding / cell junction ...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 / cell junction / lamellipodium / 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
Chem-8T5 / NITRATE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionMar 4, 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 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
B: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,23311
Polymers25,2572
Non-polymers1,9779
Water3,459192
1
A: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5134
Polymers12,6281
Non-polymers8843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7217
Polymers12,6281
Non-polymers1,0926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.715, 43.364, 44.181
Angle α, β, γ (deg.)60.97, 84.19, 84.16
Int Tables number1
Space group name H-MP1

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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 / Plasmid: pGEX-4T-1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8N8S7

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Non-polymers , 5 types, 201 molecules

#2: Chemical ChemComp-8T5 / (1~{S},4~{S},7~{R},10~{R})-14-[(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]carbonyl-2-oxidanylidene-3,14-diazatricyclo[8.4.0.0^{3,7}]tetradec-8-ene-4-carboxylic acid


Mass: 692.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H42ClN5O7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.9M ammonium sulfate, 200mM ammonium 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 PILATUS3 2M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.4→38.56 Å / Num. obs: 41864 / % possible obs: 94.6 % / Redundancy: 2.3 % / CC1/2: 0.999 / Rrim(I) all: 0.073 / Net I/σ(I): 10.39
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.12 / Num. unique obs: 6668 / CC1/2: 0.602 / Rrim(I) all: 0.995 / % possible all: 93.3

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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: 1.4→38.56 Å / Cross valid method: FREE R-VALUE / σ(F): 10.43 / Phase error: 35.76
RfactorNum. reflection% reflection
Rfree0.2575 2195 5.24 %
Rwork0.2188 --
obs0.2753 41862 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 134 192 2082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092016
X-RAY DIFFRACTIONf_angle_d1.1562747
X-RAY DIFFRACTIONf_dihedral_angle_d13.915904
X-RAY DIFFRACTIONf_chiral_restr0.076282
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3998-1.43240.40141360.34492576X-RAY DIFFRACTION88
1.4324-1.46820.31771380.32472623X-RAY DIFFRACTION89
1.4682-1.50790.3481390.32132642X-RAY DIFFRACTION89
1.5079-1.55220.30581380.30152616X-RAY DIFFRACTION89
1.5522-1.60240.32631390.29282640X-RAY DIFFRACTION90
1.6024-1.65960.28381400.28592660X-RAY DIFFRACTION90
1.6596-1.72610.30111390.27932638X-RAY DIFFRACTION90
1.7261-1.80460.29231390.27792655X-RAY DIFFRACTION91
1.8046-1.89980.29631400.27762651X-RAY DIFFRACTION90
1.8998-2.01880.28441420.27092693X-RAY DIFFRACTION91
2.0188-2.17460.31231400.26922672X-RAY DIFFRACTION91
2.1746-2.39350.29791390.2652641X-RAY DIFFRACTION91
2.3935-2.73970.28081430.25752702X-RAY DIFFRACTION92
2.7397-3.45140.28661410.24432688X-RAY DIFFRACTION91
3.4514-37.8590.35121410.27822670X-RAY DIFFRACTION91
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)
10.0090.00230.00430.0045-0.00060.00250.00460.00660.0109-0.0014-0.0007-0.0014-0.0052-0.0065-0.04780.05310.01040.02320.14690.07270.17841.663737.5809-10.8172
20.00410.00170.0050.00070.0020.0062-0.00120.0051-0.0089-0.0001-0.00050.00930.0003-0.0053-0.00330.06290.01310.00630.15740.07930.18313.10117.9907-6.7688
30.0102-0.0091-0.00330.00810.00280.0010.002-0.00710.0275-0.00130.0016-0.0091-0.0043-0.00680.02710.05040.00670.02030.15010.07330.19271.362839.2322-9.388
40.0648-0.0193-0.02770.00740.01330.02750.00690.00470.0101-0.00430.00930.0039-0.0042-0.0120.03560.0530.00520.01140.17340.07050.1995-5.18834.9233-8.4906
50.02660.0130.02020.01750.02950.0491-0.0021-0.00830.0027-0.0017-0.0107-0.00250.00320.002-0.02440.06240.020.020.18830.06010.215913.827532.0235-13.0432
60.0150.00070.0004-00.00180.0226-0.0071-0.0018-0.02230.003-0.0054-0.00880.0054-0.00230.00240.060.01210.02670.16830.08850.17637.484428.7166-10.5258
70.0033-0.001-0.00210.0011-0.00010.00220.00090.00430.0065-0.0009-0.0059-0.0016-0.0024-0.00130.02290.04370.00330.00260.1610.07950.161411.463539.006-17.7693
80.01230.00090.01690.0258-0.01520.03410.0020.00080.01750.0049-0.0040.0016-0.01170.0008-0.01590.09930.0090.05740.22950.03990.2793-10.479351.0151-19.5644
90.02940.0011-0.00150.0070.00460.0096-0.00850.008-0.00540.00070.007-0.00380.00290.00060.00570.06480.0270.02650.18460.07230.1605-8.630240.8425-36.816
100.0002-0.0003-0.00030.00730.00680.0064-0.00130.0084-0.0049-0.00020.0075-0.00740.00470.0089-0.00370.09420.0180.00780.26070.11520.1989-10.307940.8078-46.9274
110.0766-0.0128-0.01740.040.02550.03310.0051-0.00490.0469-0.0025-0.01010.0145-0.0038-0.0015-0.0440.07730.02740.03170.19390.09380.2055-6.542546.4892-28.1527
120.0336-0.0155-0.01650.02260.01660.01330.0065-0.00260.02520.0050.0090.0058-0.01340.0026-0.02840.06620.02680.04190.15520.04460.1976-11.518853.7225-25.5402
130.0004-0.00060.00060.0190.00780.0195-0.0029-0.01250.029-0.00550.0234-0.0139-0.00190.00380.0580.06080.01980.02770.2270.09680.2022-11.43444.7703-31.4614
140.0135-0.01580.00880.0191-0.01220.00930.0065-0.01160.0127-0.00160.01030.0033-0.0069-0.02030.01560.07420.03610.03280.26560.12780.1872-16.700443.0268-29.6473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 63 )
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 93 )
7X-RAY DIFFRACTION7chain 'A' and (resid 94 through 111 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 8 )
9X-RAY DIFFRACTION9chain 'B' and (resid 9 through 17 )
10X-RAY DIFFRACTION10chain 'B' and (resid 18 through 25 )
11X-RAY DIFFRACTION11chain 'B' and (resid 26 through 40 )
12X-RAY DIFFRACTION12chain 'B' and (resid 41 through 52 )
13X-RAY DIFFRACTION13chain 'B' and (resid 53 through 76 )
14X-RAY DIFFRACTION14chain 'B' and (resid 77 through 111 )

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