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- PDB-5nbx: ENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-9]-OH -

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Basic information

Entry
Database: PDB / ID: 5nbx
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-PP-[ProM-9]-OH
Components
  • ACY-2L5-PRO-PRO-8SN
  • 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
BROMIDE ION / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Oct 26, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id
Revision 2.1Feb 7, 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
C: ACY-2L5-PRO-PRO-8SN
D: ACY-2L5-PRO-PRO-8SN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6415
Polymers26,5614
Non-polymers801
Water4,107228
1
A: Protein enabled homolog
C: ACY-2L5-PRO-PRO-8SN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3603
Polymers13,2802
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein enabled homolog
D: ACY-2L5-PRO-PRO-8SN


Theoretical massNumber of molelcules
Total (without water)13,2802
Polymers13,2802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.214, 131.615, 35.704
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-201-

BR

21A-390-

HOH

31B-378-

HOH

41B-389-

HOH

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Components

#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
#2: Protein/peptide ACY-2L5-PRO-PRO-8SN


Mass: 652.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.0M ammonium sulfate, 300mM potassium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.65→45 Å / Num. obs: 25469 / % possible obs: 97.3 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rrim(I) all: 0.086 / Net I/σ(I): 12.73
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.58 / Num. unique all: 3536 / Num. unique obs: 3505 / CC1/2: 0.607 / Rrim(I) all: 0.746 / % possible all: 85.3

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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: 1.65→32.19 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.06
RfactorNum. reflection% reflection
Rfree0.1953 1274 5 %
Rwork0.1665 --
obs0.168 25465 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 95 228 2068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011940
X-RAY DIFFRACTIONf_angle_d1.2562643
X-RAY DIFFRACTIONf_dihedral_angle_d19.0021281
X-RAY DIFFRACTIONf_chiral_restr0.06277
X-RAY DIFFRACTIONf_plane_restr0.008346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6499-1.7160.26871180.30782232X-RAY DIFFRACTION82
1.716-1.79410.30731350.24262578X-RAY DIFFRACTION95
1.7941-1.88870.24451430.19962716X-RAY DIFFRACTION100
1.8887-2.0070.20071430.17882713X-RAY DIFFRACTION100
2.007-2.16190.17891440.15732731X-RAY DIFFRACTION100
2.1619-2.37940.2111460.14812769X-RAY DIFFRACTION100
2.3794-2.72360.19071440.15882748X-RAY DIFFRACTION100
2.7236-3.43080.17021470.15162780X-RAY DIFFRACTION100
3.4308-32.19640.18021540.15592924X-RAY DIFFRACTION100
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)
10.20510.1764-0.00240.2504-0.28530.85280.0856-0.2983-0.0011-0.0125-0.03870.05530.01510.04590.00010.111-0.0156-0.00030.1552-0.00660.1051-9.5094-11.612313.2398
20.215-0.32830.01530.5476-0.05270.0115-0.0459-0.05730.1168-0.01070.28480.2767-0.065-0.99990.1470.1427-0.02130.00440.39390.05870.1799-27.9201-7.942714.0978
30.0474-0.0199-0.11210.4572-0.13490.3167-0.0167-0.4389-0.13940.02660.0572-0.02880.03610.3116-0.00160.1619-0.0031-0.00030.1932-0.00170.1694-8.4401-14.098415.9501
40.42820.01450.1670.510.01040.088-0.1945-0.1436-0.28090.1636-0.06940.03980.62160.1488-0.06980.27490.0510.04870.15110.01770.2042-6.7987-21.34769.4057
50.2556-0.0964-0.20560.11490.06620.1663-0.1658-0.5781-0.40890.13820.0591-0.07330.08770.7741-0.040.19170.0136-0.01930.39240.08170.2092-9.9144-14.172425.9526
60.0241-0.03690.01150.0439-0.03080.0673-0.24410.0649-0.2608-0.16660.06570.1906-0.112-0.30130.00090.2138-0.0274-0.00570.16010.00440.1993-13.6939-18.805513.1563
70.1433-0.17870.02870.15040.04040.2060.03650.08560.0828-0.1578-0.0574-0.188-0.1476-0.0481-0.00010.158-0.00040.02330.1587-0.00910.141-13.39-8.84392.2295
80.1547-0.0458-0.03120.20640.19480.20190.0751-0.16940.0447-0.1266-0.1380.06390.0828-0.0599-0.00930.1511-0.0170.01150.12480.01560.1102-19.312-12.45686.9152
90.2487-0.31010.01090.3861-0.10710.40640.0913-0.06890.07870.1350.11260.01320.0528-0.00060.08890.1598-0.00080.01010.1586-0.02410.1398-14.0734-6.945411.781
100.5349-0.2116-0.32610.2996-0.05030.96380.04880.01210.19090.11870.1578-0.19030.11930.05030.08270.12340.00080.01990.1685-0.02760.1878-5.2256-9.14422.6943
110.64240.2841-0.4410.4310.28240.582-0.13190.2711-0.10260.00890.1733-0.03520.15-0.06550.03170.1973-0.04870.00290.1787-0.00290.1652-30.4914-19.809-8.5787
121.45490.58680.13130.4291-0.30530.587-0.20760.4312-0.541-0.27360.2175-0.13040.4425-0.1079-0.08760.3346-0.03290.07980.2202-0.05410.3117-31.6128-28.253-8.2934
130.5809-0.08450.660.0378-0.13940.81570.07890.1547-0.0482-0.4470.2838-0.30810.18870.15761.01440.4737-0.28140.09580.664-0.36430.1624-32.5185-24.3921-21.5575
140.63780.6663-0.05910.64570.0910.4833-0.11670.0292-0.1758-0.0470.0514-0.03080.1386-0.0468-0.07850.1726-0.01240.04020.19420.00020.2205-32.0812-20.3532-1.1099
150.18160.2138-0.17240.3379-0.12420.2844-0.01790.2234-0.2107-0.05780.0546-0.02610.0529-0.0458-0.0050.1133-0.01950.00090.1809-0.00190.1438-30.6187-16.4522-4.2506
160.70810.2165-0.35340.208-0.12331.1372-0.09340.0971-0.368-0.0311-0.053-0.00490.3945-0.0588-0.22990.1755-0.03220.04350.16660.02270.2383-39.3251-24.95660.9362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 40 )
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 57 )
6X-RAY DIFFRACTION6chain 'A' and (resid 58 through 63 )
7X-RAY DIFFRACTION7chain 'A' and (resid 64 through 76 )
8X-RAY DIFFRACTION8chain 'A' and (resid 77 through 85 )
9X-RAY DIFFRACTION9chain 'A' and (resid 86 through 93 )
10X-RAY DIFFRACTION10chain 'A' and (resid 94 through 111 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 25 )
12X-RAY DIFFRACTION12chain 'B' and (resid 26 through 52 )
13X-RAY DIFFRACTION13chain 'B' and (resid 53 through 57 )
14X-RAY DIFFRACTION14chain 'B' and (resid 58 through 76 )
15X-RAY DIFFRACTION15chain 'B' and (resid 77 through 93 )
16X-RAY DIFFRACTION16chain 'B' and (resid 94 through 111 )

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