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- PDB-5u1q: Grb7-SH2 with bicyclic peptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 5u1q
TitleGrb7-SH2 with bicyclic peptide inhibitor
Components
  • Growth factor receptor-bound protein 7
  • LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
KeywordsSIGNALING PROTEIN/PEPTIDE INHIBITOR / Grb7 / SH2 domain / inhibitor / signalling / SIGNALING PROTEIN-PEPTIDE INHIBITOR complex
Function / homology
Function and homology information


GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / stress granule assembly / Tie2 Signaling / Downstream signal transduction / phosphatidylinositol binding / cell projection / epidermal growth factor receptor signaling pathway / Signaling by SCF-KIT ...GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / stress granule assembly / Tie2 Signaling / Downstream signal transduction / phosphatidylinositol binding / cell projection / epidermal growth factor receptor signaling pathway / Signaling by SCF-KIT / cytoplasmic stress granule / negative regulation of translation / positive regulation of cell migration / focal adhesion / protein kinase binding / RNA binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Growth factor receptor-bound protein 7 / : / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...Growth factor receptor-bound protein 7 / : / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / SH2 domain / SHC Adaptor Protein / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsWatson, G.M. / Wilce, M.C.J. / Wilce, J.A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery, Development, and Cellular Delivery of Potent and Selective Bicyclic Peptide Inhibitors of Grb7 Cancer Target.
Authors: Watson, G.M. / Kulkarni, K. / Sang, J. / Ma, X. / Gunzburg, M.J. / Perlmutter, P. / Wilce, M.C.J. / Wilce, J.A.
History
DepositionNov 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
L: LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
M: LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
N: LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
P: LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,55312
Polymers59,4128
Non-polymers1424
Water2,432135
1
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
L: LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
M: LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8127
Polymers29,7064
Non-polymers1063
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
N: LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
P: LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7415
Polymers29,7064
Non-polymers351
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.180, 47.090, 94.610
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Growth factor receptor-bound protein 7 / B47 / Epidermal growth factor receptor GRB-7 / GRB7 adapter protein


Mass: 13690.711 Da / Num. of mol.: 4 / Fragment: UNP residues 438-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14451
#2: Protein/peptide
LYS-PHE-GLU-GLY-TYR-ASP-ASN-GLU-CST


Mass: 1162.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 6000, MES, CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→39.671 Å / Num. obs: 30704 / % possible obs: 97.7 % / Redundancy: 2.5 % / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.1→39.671 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 1554 5.06 %
Rwork0.1871 --
obs0.1898 30689 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 4 135 3690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053632
X-RAY DIFFRACTIONf_angle_d0.8134879
X-RAY DIFFRACTIONf_dihedral_angle_d7.3532122
X-RAY DIFFRACTIONf_chiral_restr0.051529
X-RAY DIFFRACTIONf_plane_restr0.005633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.34581300.27412645X-RAY DIFFRACTION98
2.1678-2.24530.28651640.24442614X-RAY DIFFRACTION98
2.2453-2.33520.29341480.22392636X-RAY DIFFRACTION98
2.3352-2.44140.29241530.21582597X-RAY DIFFRACTION98
2.4414-2.57010.30021280.21382667X-RAY DIFFRACTION98
2.5701-2.73110.30171290.21422647X-RAY DIFFRACTION98
2.7311-2.94190.2861530.21442657X-RAY DIFFRACTION98
2.9419-3.23780.28161390.19472632X-RAY DIFFRACTION97
3.2378-3.70610.20641140.16622679X-RAY DIFFRACTION97
3.7061-4.66810.1791300.14592629X-RAY DIFFRACTION95
4.6681-39.6780.21361660.17532732X-RAY DIFFRACTION98
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)
10.01950.0068-0.00310.0058-0.01080.0061-0.04680.05870.03440.10980.0870.21060.1648-0.2516-00.1698-0.0792-0.00950.22520.01320.2706-1.69514.5434139.3407
2-0.00160.0089-0.02310.011-0.01140.02480.37440.05760.04730.47380.1730.12390.3184-0.1694-0-0.00820.02620.07490.16040.05920.2834-1.068520.5754138.5888
30.0056-0.002-0.0194-0.011-0.00190.0190.13220.1098-0.02760.2-0.1032-0.0159-0.0868-0.181900.176-0.0254-0.03420.14170.06490.21295.507421.1448142.7277
40.03980.13450.00720.09740.05070.06010.14210.0728-0.1430.02370.0722-0.0499-0.52880.4931-00.20110.14810.0053-0.31690.18120.06113.552930.7887132.882
50.0019-0.0038-0.00410.01020.0071-0.0035-0.06510.0353-0.19810.0043-0.04650.15040.10360.0702-00.22720.0301-0.02790.2297-0.01410.25138.769215.7883134.8533
60.00840.00370.0050.00270.02050.01890.19070.0861-0.2486-0.1382-0.0206-0.0007-0.1797-0.0457-00.27430.0238-0.00930.37090.02450.203415.748230.7961108.3576
70.0018-0.00380.0023-0.0001-0.00440.00240.10140.06070.0486-0.31110.0765-0.0232-0.01830.0208-00.4747-0.1853-0.01420.41730.4182-0.020117.458846.1168105.4705
80.01470.03290.02710.00660.00340.0031-0.05990.1216-0.1211-0.08490.112-0.0765-0.1644-0.0505-00.21880.03060.0060.21130.11230.166713.641542.3992111.518
90.00030.00920.0029-0.0010.00050.0051-0.10960.00810.0416-0.0203-0.022-0.0147-0.090.0581-00.2735-0.06660.06170.5661-0.05510.442528.991533.1865112.1533
100.04750.025-0.06880.0111-0.00670.0053-0.02160.2186-0.2544-0.05810.3205-0.1299-0.39590.215900.23270.05840.04180.08940.12770.080119.007641.1498117.633
110.0196-0.0042-0.02060.01360.00560.0229-0.0201-0.024-0.19910.01320.0646-0.0248-0.11090.162200.197-0.0103-0.00890.1614-0.01480.20320.060229.5267125.7911
12-0.0022-0.005-0.00240.0014-0.00820.0029-0.06570.1167-0.03140.10260.2617-0.01-0.1394-0.043100.13940.06810.00020.20520.07170.16099.828333.3626120.8776
13-0.0142-0.0132-0.01370.0158-0.0112-0.00110.11820.16370.22090.04610.28550.1806-0.16510.051-00.09570.4946-0.2917-1.25191.204-0.47199.47742.3908119.0923
140.00040.00140.0020.0041-0.00220.0006-0.00090.0083-0.0396-0.00090.02260.01140.02290.028500.3465-0.0533-0.0840.40510.05130.3253-8.119719.3572126.0694
150.0037-0.00520.00440.0090.00210.0086-0.2657-0.06430.10380.3615-0.1961-0.00850.0215-0.036300.337-0.0786-0.00880.44380.0150.2164-15.473524.9555125.6772
160.0020.0045-0.00930.00160.01270.0057-0.2254-0.25790.20020.03830.08-0.1104-0.1671-0.198200.32210.02440.00960.3458-0.10630.3289-22.338534.8803122.1176
17-0.00010.004-0.0125-0.0049-0.00260.0073-0.0393-0.21680.04090.01320.03520.06090.03770.0968-00.2738-0.03750.05530.27460.08780.2571-20.465819.7824122.6774
180.0042-0.0038-0.01020.00010.00080.01270.1656-0.09590.16270.07310.01830.0571-0.032-0.054700.17760.04470.02910.230.0060.2265-20.84530.2333115.3988
190.03510.0401-0.00840.0095-0.00870.04190.0851-0.0948-0.01390.0986-0.1395-0.14990.0732-0.1614-00.2468-0.0194-0.00550.25750.08450.2606-17.784917.6969113.3096
200.0052-0.0017-0.00050.0051-0.00020.0054-0.12060.0989-0.1339-0.1223-0.12270.0980.0256-0.118800.1922-0.0507-0.02940.21990.0550.2169-13.70816.7503108.2027
21-0.0064-0.0024-0.0051-0.0031-0.00770.00130.091-0.016-0.0236-0.03080.0605-0.1049-0.0387-0.035500.1616-0.0459-0.06460.21380.00880.217-8.801123.8202113.0314
220.01310.0091-0.00150.0072-0.00840.00710.1489-0.05750.2669-0.06920.0136-0.1266-0.0737-0.031300.126-0.04060.02450.2141-0.04570.1976-13.58332.054111.962
230.005200.0040.00990.00130.00030.07790.0558-0.0637-0.05090.0862-0.03610.00720.0635-00.24640.04260.00040.35120.10560.28613.874119.5871103.6203
240.0038-0.0077-0.0099-0.001-0.00140.0006-0.00010.0811-0.08940.079-0.0032-0.06590.05870.055900.21910.47910.07010.5524-0.01540.395915.571412.37695.3434
250.00210.00180.00540.00470.0003-0.00150.0026-0.0068-0.0444-0.00650.0135-0.00920.0517-0.0396-00.63480.20370.072-0.28550.09281.12946.78596.648997.8346
260.00550.005-0.0046-0.0058-0.0288-0.01650.09210.1736-0.1349-0.0290.1822-0.0514-0.01140.348700.0979-0.09670.01290.22560.12010.250911.546624.552197.9008
270.02230.0294-0.00030.0045-0.00340.0309-0.01050.4089-0.1085-0.0192-0.15330.0083-0.14510.2504-00.14150.07030.00490.153-0.05920.16414.372621.000395.4057
280.00690.00070.00020.00150.0007-0.0023-0.04410.02390.05570.0359-0.08290.0073-0.09450.0518-00.2278-0.0018-0.06630.1886-0.01310.24840.008734.6611104.4196
290.02080.0125-0.00760.0131-0.00180.00450.02780.0697-0.0239-0.0303-0.0510-0.0325-0.0138-00.2621-0.0086-0.02150.2070.03780.1893-3.018328.6415101.1104
30-0.0026-0.00130.00270.0011-0.0031-0-0.1049-0.0784-0.1442-0.0297-0.10510.0433-0.0630.050500.1213-0.0125-0.00580.1580.03240.1823-1.083619.5604106.403
31-0.0030.0044-0.00120.0104-0.01170.003-0.0143-0.0083-0.2190.0161-0.0284-0.09590.0617-0.0841-00.24480.0363-0.10630.19120.02470.3123-0.481713.336599.9248
320.00040.00220.00720.00130.00430.00040.1109-0.13230.03980.0850.08660.00920.0792-0.1586-00.49490.30190.1784-0.08460.25030.2538-0.303632.0953145.3984
33-0.0013-0.00020.0040.0013-0.00020.0048-0.1377-0.00130.20390.0501-0.1057-0.0202-0.24640.057700.2643-0.07090.05040.27870.05020.283426.108443.5327122.4021
340.00690.00130.00430.00120.00690.0004-0.19630.05850.05310.0613-0.18590.0409-0.0309-0.086800.2276-0.0551-0.02880.27450.0010.2526-27.163220.9496110.0995
350.0032-0.00140.00440.00350.00430.0046-0.01530.0590.0088-0.1076-0.01330.0532-0.03430.1088-00.2580.0444-0.00260.27870.00490.20252.979825.573988.5236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 429 through 448 )
2X-RAY DIFFRACTION2chain 'A' and (resid 449 through 466 )
3X-RAY DIFFRACTION3chain 'A' and (resid 467 through 476 )
4X-RAY DIFFRACTION4chain 'A' and (resid 477 through 522 )
5X-RAY DIFFRACTION5chain 'A' and (resid 523 through 528 )
6X-RAY DIFFRACTION6chain 'B' and (resid 422 through 437 )
7X-RAY DIFFRACTION7chain 'B' and (resid 438 through 448 )
8X-RAY DIFFRACTION8chain 'B' and (resid 449 through 459 )
9X-RAY DIFFRACTION9chain 'B' and (resid 460 through 466 )
10X-RAY DIFFRACTION10chain 'B' and (resid 467 through 487 )
11X-RAY DIFFRACTION11chain 'B' and (resid 488 through 504 )
12X-RAY DIFFRACTION12chain 'B' and (resid 505 through 514 )
13X-RAY DIFFRACTION13chain 'B' and (resid 515 through 528 )
14X-RAY DIFFRACTION14chain 'C' and (resid 423 through 428 )
15X-RAY DIFFRACTION15chain 'C' and (resid 429 through 437 )
16X-RAY DIFFRACTION16chain 'C' and (resid 438 through 454 )
17X-RAY DIFFRACTION17chain 'C' and (resid 455 through 466 )
18X-RAY DIFFRACTION18chain 'C' and (resid 467 through 475 )
19X-RAY DIFFRACTION19chain 'C' and (resid 476 through 494 )
20X-RAY DIFFRACTION20chain 'C' and (resid 495 through 504 )
21X-RAY DIFFRACTION21chain 'C' and (resid 505 through 512 )
22X-RAY DIFFRACTION22chain 'C' and (resid 513 through 528 )
23X-RAY DIFFRACTION23chain 'D' and (resid 429 through 437 )
24X-RAY DIFFRACTION24chain 'D' and (resid 438 through 447 )
25X-RAY DIFFRACTION25chain 'D' and (resid 448 through 454 )
26X-RAY DIFFRACTION26chain 'D' and (resid 455 through 466 )
27X-RAY DIFFRACTION27chain 'D' and (resid 467 through 487 )
28X-RAY DIFFRACTION28chain 'D' and (resid 488 through 494 )
29X-RAY DIFFRACTION29chain 'D' and (resid 495 through 504 )
30X-RAY DIFFRACTION30chain 'D' and (resid 505 through 514 )
31X-RAY DIFFRACTION31chain 'D' and (resid 515 through 528 )
32X-RAY DIFFRACTION32chain 'L' and (resid 1 through 8 )
33X-RAY DIFFRACTION33chain 'M' and (resid 1 through 8 )
34X-RAY DIFFRACTION34chain 'N' and (resid 1 through 8 )
35X-RAY DIFFRACTION35chain 'P' and (resid 1 through 8 )

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