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- PDB-5tyi: Grb7 SH2 with bicyclic peptide containing pY mimetic -

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Basic information

Entry
Database: PDB / ID: 5tyi
TitleGrb7 SH2 with bicyclic peptide containing pY mimetic
Components
  • Growth factor receptor-bound protein 7
  • Peptide inhibitor
KeywordsSignaling Protein/Peptide / SH2 / inhibitor / bicyclic / Signaling Protein-Peptide complex
Function / homology
Function and homology information


GRB7 events in ERBB2 signaling / RND1 GTPase cycle / RET signaling / stress granule assembly / Tie2 Signaling / phosphatidylinositol binding / Downstream signal transduction / 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 / phosphatidylinositol binding / Downstream signal transduction / 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: 2.15 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 20, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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: Peptide inhibitor
M: Peptide inhibitor
N: Peptide inhibitor
P: Peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)59,5248
Polymers59,5248
Non-polymers00
Water2,198122
1
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
N: Peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)28,5723
Polymers28,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Growth factor receptor-bound protein 7
D: Growth factor receptor-bound protein 7
L: Peptide inhibitor
M: Peptide inhibitor
P: Peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)30,9525
Polymers30,9525
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.070, 107.610, 48.012
Angle α, β, γ (deg.)90.00, 101.38, 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
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
Peptide inhibitor


Mass: 1190.216 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, NaSCN

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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: 2.15→44.184 Å / Num. obs: 24095 / % possible obs: 98.7 % / Redundancy: 2.8 % / Net I/σ(I): 4.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementResolution: 2.15→44.184 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1195 4.97 %
Rwork0.2066 --
obs0.2087 24038 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→44.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 0 122 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093607
X-RAY DIFFRACTIONf_angle_d1.2564839
X-RAY DIFFRACTIONf_dihedral_angle_d15.0331265
X-RAY DIFFRACTIONf_chiral_restr0.06530
X-RAY DIFFRACTIONf_plane_restr0.006632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.23610.32311310.25332501X-RAY DIFFRACTION98
2.2361-2.33790.29751200.25522516X-RAY DIFFRACTION97
2.3379-2.46110.28651330.24932522X-RAY DIFFRACTION98
2.4611-2.61530.34891200.24672532X-RAY DIFFRACTION98
2.6153-2.81720.26641320.23672565X-RAY DIFFRACTION98
2.8172-3.10060.24351370.21552508X-RAY DIFFRACTION99
3.1006-3.54910.21561220.18452558X-RAY DIFFRACTION99
3.5491-4.47090.20311510.16682556X-RAY DIFFRACTION99
4.4709-44.19320.22991490.19052585X-RAY DIFFRACTION99

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