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- PDB-5naj: ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-1]-[ProM-1]-OH -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5naj
TitleENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-1]-[ProM-1]-OH
ComponentsProtein 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
Chem-8SB / Chem-8SE / Protein enabled homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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
DepositionFeb 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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
C: Protein enabled homolog
D: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,80419
Polymers50,5134
Non-polymers4,29115
Water4,648258
1
A: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5955
Polymers12,6281
Non-polymers9664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2736
Polymers12,6281
Non-polymers1,6455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4994
Polymers12,6281
Non-polymers8703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein enabled homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4384
Polymers12,6281
Non-polymers8103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.954, 80.766, 73.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-304-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Protein enabled homolog


Mass: 12628.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Mismatch of S2A: only backbone of N-terminus was resolved and modelled
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, 273 molecules

#2: Chemical
ChemComp-8SE / (3~{S},7~{R},10~{R},13~{S})-4-[[(3~{S},7~{R},10~{R},13~{S})-4-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-en-13-yl]carbonyl]-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid


Mass: 678.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H40ClN5O7
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-8SB / (3~{S},7~{R},10~{R},13~{S})-4-[[(3~{R},7~{S},10~{S},13~{R})-4-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-en-13-yl]carbonyl]-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid


Mass: 678.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40ClN5O7
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2M ammonium sulfate, 200mM ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.46→44.6 Å / Num. obs: 81310 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rrim(I) all: 0.09 / Net I/σ(I): 11.79
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 5.5 % / CC1/2: 0.621 / Rrim(I) all: 1.01 / % possible all: 99.6

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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: 1.46→40.383 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.24
RfactorNum. reflection% reflection
Rfree0.2001 4066 5 %
Rwork0.1786 --
obs0.1797 81304 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→40.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 286 258 4016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083946
X-RAY DIFFRACTIONf_angle_d1.285396
X-RAY DIFFRACTIONf_dihedral_angle_d15.2921833
X-RAY DIFFRACTIONf_chiral_restr0.084564
X-RAY DIFFRACTIONf_plane_restr0.007701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4582-1.47540.30711370.2782603X-RAY DIFFRACTION98
1.4754-1.49340.31971380.25992619X-RAY DIFFRACTION100
1.4934-1.51230.27471380.24982623X-RAY DIFFRACTION100
1.5123-1.53220.27761390.2482645X-RAY DIFFRACTION100
1.5322-1.55320.25451390.23882638X-RAY DIFFRACTION100
1.5532-1.57540.27111380.2282620X-RAY DIFFRACTION100
1.5754-1.59890.24271410.20762675X-RAY DIFFRACTION100
1.5989-1.62390.23661380.21652618X-RAY DIFFRACTION100
1.6239-1.65050.24951390.20972652X-RAY DIFFRACTION100
1.6505-1.67890.27241390.21072636X-RAY DIFFRACTION100
1.6789-1.70950.23091390.19952648X-RAY DIFFRACTION100
1.7095-1.74230.24941390.19432631X-RAY DIFFRACTION100
1.7423-1.77790.21731400.18522658X-RAY DIFFRACTION100
1.7779-1.81660.18851390.18352653X-RAY DIFFRACTION100
1.8166-1.85880.22511390.17722636X-RAY DIFFRACTION100
1.8588-1.90530.19451410.15862669X-RAY DIFFRACTION100
1.9053-1.95680.1811380.16332640X-RAY DIFFRACTION100
1.9568-2.01440.17941400.16112659X-RAY DIFFRACTION100
2.0144-2.07940.18961400.16172658X-RAY DIFFRACTION100
2.0794-2.15370.18011410.16312676X-RAY DIFFRACTION100
2.1537-2.240.19261410.16422680X-RAY DIFFRACTION100
2.24-2.34190.17781400.16452647X-RAY DIFFRACTION100
2.3419-2.46540.18411400.17052675X-RAY DIFFRACTION100
2.4654-2.61980.2051420.17582690X-RAY DIFFRACTION100
2.6198-2.8220.2031410.18732686X-RAY DIFFRACTION100
2.822-3.10590.20381420.18252698X-RAY DIFFRACTION99
3.1059-3.55510.20751430.172715X-RAY DIFFRACTION99
3.5551-4.47820.1431440.14952736X-RAY DIFFRACTION99
4.4782-40.39850.19551510.18162854X-RAY DIFFRACTION99
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)
14.18174.28892.34644.60653.0085.13450.1765-0.3517-0.37150.1651-0.0479-0.47880.07480.1521-0.14980.1371-0.0202-0.02640.20790.05510.163125.394682.954824.7848
22.47991.6235-2.25033.2254-2.54625.5241-0.11220.1848-0.1273-0.24530.0709-0.13830.0966-0.09440.00490.1366-0.00090.02490.114-0.00470.105719.394380.80215.778
33.70680.9478-1.26540.65260.33211.4885-0.11140.38780.0993-0.65610.2607-0.0266-0.01260.01010.01440.2579-0.03990.07720.1612-0.0070.120722.022182.2528-2.7906
42.50131.46960.69626.62322.24414.15680.0978-0.1916-0.04580.3564-0.0096-0.4167-0.10270.3045-0.0740.1005-0.022-0.00720.20020.02660.140226.200782.697818.1514
56.18395.34931.0884.72981.26212.62190.01650.0414-0.5199-0.14480.0245-0.59470.20060.3226-0.15180.13080.01130.03250.21230.01010.181426.857176.683812.4338
65.78674.75723.92434.23822.79583.9809-0.0755-0.3116-0.01810.03760.0112-0.042-0.4035-0.12430.04550.18470.02270.01610.1196-0.00350.130317.000692.502311.9535
73.15212.1858-1.85835.0702-2.09492.55570.1414-0.00980.0982-0.0394-0.0302-0.0119-0.14690.0409-0.11750.1307-0.01230.02990.0921-0.00270.096720.177787.50667.1662
88.50545.06820.68774.06671.11143.64730.0139-0.17360.47050.231-0.03420.2189-0.2367-0.0070.05170.15560.0167-0.00980.1397-0.0020.109716.259190.056319.8463
98.85640.7077-0.79834.3544-1.22262.6865-0.09230.06140.5457-0.85510.17460.0623-0.6121-0.1734-0.06570.3128-0.0111-0.01650.1403-0.00170.13172.1016108.858111.9753
102.52320.8721.94272.0291.12416.36720.1101-0.21920.08030.3011-0.0506-0.09040.03430.1935-0.07820.1513-0.0121-0.01190.1655-0.03070.10182.1265103.528634.9781
115.82772.6679-2.70544.6298-2.10784.84350.01970.22030.4064-0.22610.0897-0.0476-0.1862-0.0046-0.10760.14460.0078-0.01220.0927-0.01090.14231.5906109.943219.0069
123.46964.31890.61836.2544-0.09962.62070.1012-0.03520.44440.12840.08390.3027-0.2845-0.2268-0.08690.16130.0287-0.00330.177-0.02460.1868-3.8109109.811324.4715
133.66232.350.24846.8308-1.94812.5139-0.02130.0403-0.136-0.1037-0.0366-0.6734-0.07090.38520.05590.1107-0.0010.00390.1658-0.0540.166213.1071101.756923.6688
144.64584.26732.10976.03821.70032.6103-0.0824-0.078600.03440.0271-0.0726-0.16950.12390.05810.1202-0.0079-0.020.1438-0.03340.11437.618103.853228.6175
158.80496.353-3.12765.7459-2.44795.4351-0.14820.1503-0.068-0.35340.1633-0.4572-0.10940.24460.02480.13050.01040.01740.1477-0.0360.174910.0146101.027815.9061
164.091-0.65950.60642.3135-0.0011.5376-0.06550.1391-0.0476-0.17840.04390.10760.0091-0.02550.02920.1287-0.0173-0.02180.10220.0030.0723-10.938794.0874-0.3638
177.25153.8657-2.13225.2216-1.06362.9026-0.07940.15520.0561-0.28530.1214-0.1298-0.05170.21550.01370.11680.00070.0050.15910.01660.1008-0.406294.4212-2.6068
184.68682.2536-2.00976.3079-4.03233.7978-0.40680.5199-0.3629-0.6930.30810.20960.3208-0.13380.08980.1656-0.02810.02240.1957-0.0340.1493-5.958986.8701-4.067
192.53490.14110.09962.1292-0.13253.0505-0.00180.00710.2966-0.1004-0.0217-0.1274-0.14130.14310.00760.1014-0.0033-0.01890.0893-0.00230.1192-6.345101.5044.9419
204.2002-0.8184.01282.64220.60744.79830.154-0.4259-0.53150.1035-0.00420.2777-0.1425-0.1839-0.15450.2020.03620.01430.26860.00320.2015-9.055475.362435.418
213.8055-1.52330.09184.8196-0.02452.71830.0247-0.26910.33780.422-0.01910.1411-0.2816-0.1156-0.020.2-0.01850.040.1775-0.06020.155-10.87699.217237.2748
226.83973.7971-0.78086.4616-0.5212.32290.0324-0.3167-0.39120.2824-0.1754-0.06580.1305-0.04890.13890.14430.02930.01930.1357-0.01150.0776-9.750181.409937.9804
237.03431.4179-6.88721.2469-1.33887.4564-0.0095-0.87360.01590.1932-0.0671-0.09520.0310.51880.01840.1660.0079-0.0170.1378-0.02360.1109-3.97887.568940.1443
246.3531.1484-2.59777.6129-4.38763.855-0.3371-0.152-0.2225-0.02030.30740.49240.2578-0.55250.04780.1516-0.03280.05080.212-0.06680.1869-23.586284.439736.0385
251.69250.0809-1.61291.82430.52264.873-0.0261-0.1530.09440.07020.02240.1083-0.119-0.13060.00420.10580.03380.00490.1793-0.04650.1063-18.20692.608733.0456
263.29120.916-0.43123.73720.93274.7656-0.1488-0.0064-0.210.02890.10650.05340.2625-0.20980.02460.11220.0326-0.00880.1443-0.01490.0941-15.248784.445628.7839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 17 )
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 28 )
4X-RAY DIFFRACTION4chain 'A' and (resid 29 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 63 )
6X-RAY DIFFRACTION6chain 'A' and (resid 64 through 76 )
7X-RAY DIFFRACTION7chain 'A' and (resid 77 through 93 )
8X-RAY DIFFRACTION8chain 'A' and (resid 94 through 111 )
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 8 )
10X-RAY DIFFRACTION10chain 'B' and (resid 9 through 28 )
11X-RAY DIFFRACTION11chain 'B' and (resid 29 through 52 )
12X-RAY DIFFRACTION12chain 'B' and (resid 53 through 63 )
13X-RAY DIFFRACTION13chain 'B' and (resid 64 through 76 )
14X-RAY DIFFRACTION14chain 'B' and (resid 77 through 93 )
15X-RAY DIFFRACTION15chain 'B' and (resid 94 through 111 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 28 )
17X-RAY DIFFRACTION17chain 'C' and (resid 29 through 52 )
18X-RAY DIFFRACTION18chain 'C' and (resid 53 through 63 )
19X-RAY DIFFRACTION19chain 'C' and (resid 64 through 111 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 8 )
21X-RAY DIFFRACTION21chain 'D' and (resid 9 through 28 )
22X-RAY DIFFRACTION22chain 'D' and (resid 29 through 52 )
23X-RAY DIFFRACTION23chain 'D' and (resid 53 through 63 )
24X-RAY DIFFRACTION24chain 'D' and (resid 64 through 70 )
25X-RAY DIFFRACTION25chain 'D' and (resid 71 through 85 )
26X-RAY DIFFRACTION26chain 'D' and (resid 86 through 111 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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