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- PDB-5u06: Grb7-SH2 with bicyclic peptide inhibitor containing a pY mimetic -

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Basic information

Entry
Database: PDB / ID: 5u06
TitleGrb7-SH2 with bicyclic peptide inhibitor containing a pY mimetic
Components
  • Growth factor receptor-bound protein 7
  • bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST
KeywordsSIGNALING PROTEIN/INHIBITOR / Grb7 / SH2 domain / inhibitor / signalling / SIGNALING PROTEIN-PEPTIDE INHIBITOR complex / SIGNALING PROTEIN-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 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / 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 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / 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, 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 22, 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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: bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST
M: bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST
N: bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST
P: bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6199
Polymers59,5808
Non-polymers391
Water3,441191
1
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
L: bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST
M: bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8295
Polymers29,7904
Non-polymers391
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
N: bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST
P: bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST


Theoretical massNumber of molelcules
Total (without water)29,7904
Polymers29,7904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.980, 109.741, 48.330
Angle α, β, γ (deg.)90.00, 103.44, 90.00
Int Tables number4
Space group name H-MP1211

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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
bicyclic peptide inhibitor: LYS-PHE-GLU-GLY-CMF-ASP-ASN-GLU-CST


Mass: 1204.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, KSCN, BTP

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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: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→35.74 Å / Num. obs: 28374 / % possible obs: 99.9 % / Redundancy: 3.6 % / Net I/σ(I): 5.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.1→35.74 Å / Cross valid method: FREE R-VALUE / σ(F): 19.8 / Phase error: 31.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2526 1404 4.95 %
Rwork0.2063 --
obs0.2153 28347 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 1 191 3887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043777
X-RAY DIFFRACTIONf_angle_d0.7165058
X-RAY DIFFRACTIONf_dihedral_angle_d9.5892204
X-RAY DIFFRACTIONf_chiral_restr0.044547
X-RAY DIFFRACTIONf_plane_restr0.003660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.34421390.2832675X-RAY DIFFRACTION95
2.1751-2.26210.33371460.27972655X-RAY DIFFRACTION95
2.2621-2.3650.30471370.26372687X-RAY DIFFRACTION95
2.365-2.48970.31191560.25832681X-RAY DIFFRACTION95
2.4897-2.64560.33621390.26012670X-RAY DIFFRACTION95
2.6456-2.84970.33311380.23542729X-RAY DIFFRACTION95
2.8497-3.13610.26131330.22552686X-RAY DIFFRACTION95
3.1361-3.58920.23191540.1882672X-RAY DIFFRACTION95
3.5892-4.51920.19731220.17082728X-RAY DIFFRACTION96
4.5192-28.87160.17931340.17212759X-RAY DIFFRACTION95
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)
10.00020.00030.00010-0.00020.0005-0.00650.0013-0.00150.0026-0.0040.00260.0037-0.001100.0338-0.0016-0.05960.08360.01040.0645-14.6357-25.3841-9.1126
20.0016-0.00090.0027-0.0030.0026-0.00060.008-0.00450.003-0.00890.00280.0036-0.0018-0.008-0-0.13250.0007-0.28960.1296-0.00090.0014-17.5275-15.3729-11.9018
30.0001-0.0010.0047-0.0060.0027-0.001-0.0162-0.0127-0.0113-0.0264-0.0137-0.02190.02320.00270-0.2277-0.0428-0.34630.11050.0492-0.0684-4.9434-15.3948-6.7613
40.0004-0.0009-0.00050.00170.0010.00060.00090.0002-0.00020.0007-0.00010.0005-0.0009-0.000100.2461-0.0074-0.01770.2438-0.00320.2495-25.0277-26.8235-6.357
50.00030.00010.00040.00020.00030.0006-0.005-0.0017-0.0028-0.0011-0.002400.00330.00100.0498-0.0073-0.04860.0902-0.00070.08038.4484-26.701115.5295
60.0005-0.00140.0015-0.00110.00040.00070.0028-0.0025-0.0032-0.00150.0014-0.00570.00110.0056-0-0.02460.0148-0.20510.12940.02920.034215.4607-20.551615.8355
70.0002-0.00030.0015-0.0020.00040.00140.00390.00350.00130.0006-0.0019-0.0031-0.00360.00860-0.0269-0.0218-0.17670.1190.01250.007211.4267-14.167311.6148
80.0007-0.0010.0031-0.0024-0.00060.00030.00480.0050.00350.0063-0.00890.00960.00020.00740-0.0442-0.0109-0.25440.12830.04410.05252.5832-14.58036.2
90.0004-0.0010.0010.0031-0.00220.002-0.00160.0006-0.00010.0004-0.00150.00040.0017-0.0003-00.13970.0005-0.01970.15670.00210.152514.3655-26.11355.4846
10-0.00010.00060.0005-0.0004-0.0002-0.0001-0.001-0.00070.0041-0.0063-0.0026-0.0017-0.00140.0008-00.0946-0.0171-0.08450.1316-0.0310.1325.120419.89167.5308
110.0001-00.000200.00010.00040.002-0.00070.00050.00230.00020.0004-0.00130.0017-00.1162-0.0078-0.06050.1572-0.02450.126923.344315.119321.661
120.0006-00.0018-0.00060.00140.0007-0.0054-0.0009-00.0039-0.00940.0003-0.0010.001500.0076-0.0255-0.09640.0879-0.03030.023123.09813.137914.089
130.0021-0.00010.0023-0.00270.00110.00040.0011-0.01920.0037-0.0092-0.0144-0.0110.0067-0.00610-0.0163-0.0104-0.18910.0951-0.01820.010521.25767.20937.1844
14-0-0.00030.0023-0.00080.0008-0.00030.0023-0.00440.00140.0019-0.0031-0.0002-0.0021-0.003100.01730.0357-0.19090.0884-0.02550.059915.47518.91672.2149
1500.00010.00050.00020.0001-0.00020.005-0.00210.0065-0.00070.003-0.0011-0.0031-0.003500.0955-0.0149-0.04990.1373-0.03670.12614.212315.777212.8107
160.00010.000200.000100.00030.00210.00090.0025-0.00060.0020.0012-0.00040.0004-00.1375-0.032-0.04840.16110.00070.14077.134519.0477-17.6966
170.0003-0.00040.0008-0.00150.00080.0004-0.00440.00140.0023-0.0027-0.00270.0007-0.00550.001500.0179-0.0223-0.16790.13570.02810.0363.40599.9223-22.4551
180.0005-0.00180.0021-0.00150.00080.00030.00330.0030.00270.0124-0.00170.0015-0.00350.0035-0-0.0252-0.0203-0.15640.0942-0.00150.04482.21948.2511-11.9268
190.00020.00030.0012-0.0010.00030.00060.0054-0.00130.00440.00460.00250.0064-0.0060.003100.0138-0.052-0.16640.1257-0.0120.03397.652310.1649-5.4444
200.00020.00060.0008-0.0006-0.0006-0.00010.0095-0.00250.0023-0.00550.0033-0.0048-0.00060.001400.0779-0.0157-0.07120.12520.00170.078712.1775.596-15.4302
21-0.000100.00040.0001-0.00040.00010.00350.0010.0007-0.00410.0016-0.0012-0.0009-0.0003-00.0807-0.0049-0.08070.11950.01930.0858-7.0139-8.7728-17.7553
220.00010.00040.000500-0.00010.0050.00150.00230.00040.0026-0.001-0.0019-0.000900.0398-0.0205-0.0870.079-0.00470.068611.8167-6.910314.2726
23-0.0001-0.00010.00040.0005-0.00010.0002-0.0045-0.0015-0.0018-0.0002-0.0019-0.00020.0029-0.000600.1175-0.0132-0.07110.12750.01460.121622.65660.115813.4994
240.00020.00020.00030.0002-0.00020.0003-0.0041-0.0023-0.0020.0027-0.00310.00210.00150.0001-00.062-0.0273-0.07160.1282-0.00050.0872-4.28052.4865-12.766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 426 through 437 )
2X-RAY DIFFRACTION2chain 'A' and (resid 438 through 475 )
3X-RAY DIFFRACTION3chain 'A' and (resid 476 through 527 )
4X-RAY DIFFRACTION4chain 'A' and (resid 528 through 532 )
5X-RAY DIFFRACTION5chain 'B' and (resid 427 through 437 )
6X-RAY DIFFRACTION6chain 'B' and (resid 438 through 466 )
7X-RAY DIFFRACTION7chain 'B' and (resid 467 through 487 )
8X-RAY DIFFRACTION8chain 'B' and (resid 488 through 522 )
9X-RAY DIFFRACTION9chain 'B' and (resid 523 through 528 )
10X-RAY DIFFRACTION10chain 'C' and (resid 423 through 437 )
11X-RAY DIFFRACTION11chain 'C' and (resid 438 through 447 )
12X-RAY DIFFRACTION12chain 'C' and (resid 448 through 466 )
13X-RAY DIFFRACTION13chain 'C' and (resid 467 through 494 )
14X-RAY DIFFRACTION14chain 'C' and (resid 495 through 517 )
15X-RAY DIFFRACTION15chain 'C' and (resid 518 through 530 )
16X-RAY DIFFRACTION16chain 'D' and (resid 425 through 437 )
17X-RAY DIFFRACTION17chain 'D' and (resid 438 through 466 )
18X-RAY DIFFRACTION18chain 'D' and (resid 467 through 494 )
19X-RAY DIFFRACTION19chain 'D' and (resid 495 through 514 )
20X-RAY DIFFRACTION20chain 'D' and (resid 515 through 529 )
21X-RAY DIFFRACTION21chain 'L' and (resid 1 through 8 )
22X-RAY DIFFRACTION22chain 'M' and (resid 1 through 8 )
23X-RAY DIFFRACTION23chain 'N' and (resid 1 through 8 )
24X-RAY DIFFRACTION24chain 'P' and (resid 1 through 8 )

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