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- PDB-4x6s: Grb7 SH2 domain with phosphotyrosine mimetic inhibitor peptide -

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Basic information

Entry
Database: PDB / ID: 4x6s
TitleGrb7 SH2 domain with phosphotyrosine mimetic inhibitor peptide
Components
  • Growth factor receptor-bound protein 7
  • Phosphotyrosine mimetic inhibitor peptide G7-TEM1
KeywordsSignaling Protein/Inhibitor / src Homology Domain / inhibitor / phosphotyrosine binding pocket / 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: 2.55 Å
AuthorsWatson, G.M. / Panjikar, S. / Wilce, M.C. / Wilce, J.A.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Cyclic Peptides Incorporating Phosphotyrosine Mimetics as Potent and Specific Inhibitors of the Grb7 Breast Cancer Target.
Authors: Watson, G.M. / Gunzburg, M.J. / Ambaye, N.D. / Lucas, W.A. / Traore, D.A. / Kulkarni, K. / Cergol, K.M. / Payne, R.J. / Panjikar, S. / Pero, S.C. / Perlmutter, P. / Wilce, M.C. / Wilce, J.A.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth factor receptor-bound protein 7
B: Growth factor receptor-bound protein 7
L: Phosphotyrosine mimetic inhibitor peptide G7-TEM1
M: Phosphotyrosine mimetic inhibitor peptide G7-TEM1


Theoretical massNumber of molelcules
Total (without water)28,0804
Polymers28,0804
Non-polymers00
Water52229
1
A: Growth factor receptor-bound protein 7
L: Phosphotyrosine mimetic inhibitor peptide G7-TEM1


Theoretical massNumber of molelcules
Total (without water)14,0402
Polymers14,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-3 kcal/mol
Surface area6420 Å2
MethodPISA
2
B: Growth factor receptor-bound protein 7
M: Phosphotyrosine mimetic inhibitor peptide G7-TEM1


Theoretical massNumber of molelcules
Total (without water)14,0402
Polymers14,0402
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-3 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.480, 68.895, 77.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12562.474 Da / Num. of mol.: 2 / Fragment: SH2 domain containing residues 423-529
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 Phosphotyrosine mimetic inhibitor peptide G7-TEM1


Mass: 1477.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.05 M HEPES pH 7.0, 1% tryptone, 12% PEG3350

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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: Nov 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.55→43.2175 Å / Num. obs: 10038 / % possible obs: 99.53 % / Redundancy: 8.9 % / Net I/σ(I): 11.71

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 2.55→43.211 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 479 4.79 %
Rwork0.2023 --
obs0.2048 9992 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→43.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 0 29 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091908
X-RAY DIFFRACTIONf_angle_d1.1882569
X-RAY DIFFRACTIONf_dihedral_angle_d13.352661
X-RAY DIFFRACTIONf_chiral_restr0.047279
X-RAY DIFFRACTIONf_plane_restr0.006334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.91920.29141630.24613117X-RAY DIFFRACTION100
2.9192-3.67750.29771650.22953136X-RAY DIFFRACTION99
3.6775-43.21750.2071510.17483260X-RAY DIFFRACTION98

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