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- PDB-5eeq: Grb7 SH2 with the G7-B1 bicyclic peptide inhibitor -

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Basic information

Entry
Database: PDB / ID: 5eeq
TitleGrb7 SH2 with the G7-B1 bicyclic peptide inhibitor
Components
  • Bicyclic Peptide Inhibitor
  • Growth factor receptor-bound protein 7
KeywordsSignaling Protein/Inhibitor / staple / SH2 / inhibitor / 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 / 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
PHOSPHATE ION / Growth factor receptor-bound protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsAmbaye, N.D. / Watson, G.M. / Wilce, M.C.J. / Wilce, G.M.
CitationJournal: Sci Rep / Year: 2016
Title: Unexpected involvement of staple leads to redesign of selective bicyclic peptide inhibitor of Grb7.
Authors: Gunzburg, M.J. / Kulkarni, K. / Watson, G.M. / Ambaye, N.D. / Del Borgo, M.P. / Brandt, R. / Pero, S.C. / Perlmutter, P. / Wilce, M.C. / Wilce, J.A.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 2.0Apr 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues

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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
L: Bicyclic Peptide Inhibitor
M: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3286
Polymers30,1384
Non-polymers1902
Water3,063170
1
A: Growth factor receptor-bound protein 7
L: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1643
Polymers15,0692
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-9 kcal/mol
Surface area6190 Å2
MethodPISA
2
B: Growth factor receptor-bound protein 7
M: Bicyclic Peptide Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1643
Polymers15,0692
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.081, 63.811, 52.040
Angle α, β, γ (deg.)90.00, 92.50, 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.: 2 / Fragment: UNP rersidues 415-532
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


Mass: 1378.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M bis-tris pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.6→40.31 Å / Num. obs: 31961 / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 1.6→40.306 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 1604 5.03 %
Rwork0.1734 --
obs0.1746 31909 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→40.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 10 170 2027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051904
X-RAY DIFFRACTIONf_angle_d0.9352563
X-RAY DIFFRACTIONf_dihedral_angle_d13.143687
X-RAY DIFFRACTIONf_chiral_restr0.037274
X-RAY DIFFRACTIONf_plane_restr0.005331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.65170.29941470.28892725X-RAY DIFFRACTION100
1.6517-1.71070.29151550.24222733X-RAY DIFFRACTION100
1.7107-1.77920.2781470.21132748X-RAY DIFFRACTION99
1.7792-1.86020.24851600.19952729X-RAY DIFFRACTION100
1.8602-1.95830.21841250.17192767X-RAY DIFFRACTION100
1.9583-2.0810.18751360.17312762X-RAY DIFFRACTION100
2.081-2.24160.22111440.17342763X-RAY DIFFRACTION100
2.2416-2.46720.18971210.17572794X-RAY DIFFRACTION100
2.4672-2.82410.19151380.18412765X-RAY DIFFRACTION100
2.8241-3.55780.20251580.1662758X-RAY DIFFRACTION100
3.5578-40.31850.16291730.15122761X-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)
11.8619-1.50090.47047.79193.06045.7627-0.1983-0.23580.1726-0.05790.1836-1.17430.27740.9601-0.14460.18310.180.09140.55450.0330.445818.1557-2.08097.953
23.3378-2.4345-2.79728.1568-0.88753.68930.1372-0.176-0.7263-0.4408-0.0743-0.17811.57141.0384-0.14620.44090.17480.06150.2710.0140.3910.7086-13.32488.8526
32.60360.135-0.73373.2664-0.77617.0062-0.11510.0452-0.1568-0.2552-0.0481-0.190.55770.37590.17970.19460.06490.03840.2102-0.01010.21327.1891-3.0357.0155
44.17050.6232-0.37464.63440.82144.87360.02210.01370.052-0.095-0.0131-0.2222-0.05570.46340.02490.11220.02220.00330.1911-0.00750.19117.49376.942410.3358
51.86680.6975-1.11715.64961.85196.0533-0.1133-0.1120.00060.75420.0228-1.31510.11291.04560.05060.2665-0.0847-0.12230.49920.0260.479817.751727.784320.3536
63.64952.34121.75384.8172.05765.5515-0.06040.1890.38160.09050.0848-0.3475-0.99430.8408-0.10060.368-0.1318-0.03340.23480.0140.34559.323538.487414.6037
73.5618-0.42340.1292.92130.02685.3585-0.0404-0.3420.16360.4512-0.0597-0.2484-0.30620.35020.08020.2956-0.0667-0.06460.204-0.01370.22837.281630.728321.2349
85.2739-1.0139-0.02349.6336-2.39116.357-0.0133-0.228-0.28150.18040.00410.20920.2916-0.0163-0.19510.2142-0.0144-0.0150.189-0.02470.15713.704125.245122.6619
94.649-0.54760.71365.327-0.09496.6206-0.0438-0.067-0.04010.1465-0.0276-0.28660.08720.33310.0470.1339-0.0207-0.00450.1559-0.01620.19797.007919.664316.3816
103.72-3.6560.44288.56122.9242.3247-0.0217-0.0254-0.2087-0.1698-0.15180.83090.512-0.61770.20190.2303-0.033-0.00430.2365-0.01220.2685-2.7112-1.6132.6823
115.2281.0339-1.93165.90463.04332.77150.05820.17050.14360.0744-0.18350.6259-0.7473-0.6710.20430.240.04170.00310.2143-0.01230.2149-3.794228.272223.0136
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 447 )
3X-RAY DIFFRACTION3chain 'A' and (resid 448 through 487 )
4X-RAY DIFFRACTION4chain 'A' and (resid 488 through 528 )
5X-RAY DIFFRACTION5chain 'B' and (resid 424 through 437 )
6X-RAY DIFFRACTION6chain 'B' and (resid 438 through 454 )
7X-RAY DIFFRACTION7chain 'B' and (resid 455 through 475 )
8X-RAY DIFFRACTION8chain 'B' and (resid 476 through 487 )
9X-RAY DIFFRACTION9chain 'B' and (resid 488 through 527 )
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 10 )
11X-RAY DIFFRACTION11chain 'M' and (resid 1 through 10 )

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