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- PDB-1b07: CRK SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1b07
TitleCRK SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR
Components
  • PROTEIN (PROTO-ONCOGENE CRK (CRK))
  • PROTEIN (SH3 PEPTOID INHIBITOR)
KeywordsSH3 DOMAIN / INHIBITORS / PEPTOIDS / PROTEIN-PROTEIN RECOGNITION / PROLINE-RICH MOTIFS / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / SHC-related events triggered by IGF1R ...Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / SHC-related events triggered by IGF1R / SOS-mediated signalling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates RAS signaling / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / Tie2 Signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Interleukin-15 signaling / FLT3 Signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / NCAM signaling for neurite out-growth / Regulation of KIT signaling / Role of LAT2/NTAL/LAB on calcium mobilization / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / regulation of leukocyte migration / response to peptide / Downstream signal transduction / regulation of intracellular signal transduction / postsynaptic specialization assembly / Insulin receptor signalling cascade / FCERI mediated MAPK activation / lymphocyte homeostasis / Signal attenuation / NRAGE signals death through JNK / protein phosphorylated amino acid binding / Signaling by SCF-KIT / RAC1 GTPase cycle / regulation of T cell migration / GRB2:SOS provides linkage to MAPK signaling for Integrins / p130Cas linkage to MAPK signaling for integrins / FCERI mediated Ca+2 mobilization / reelin-mediated signaling pathway / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / G alpha (12/13) signalling events / regulation of dendrite development / midbrain morphogenesis / positive regulation of skeletal muscle acetylcholine-gated channel clustering / regulation of pro-B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to yeast / Regulation of signaling by CBL / regulation of Rac protein signal transduction / vitellogenesis / Regulation of actin dynamics for phagocytic cup formation / negative regulation of wound healing / pericardium morphogenesis / cardiac atrium morphogenesis / RET signaling / heart trabecula morphogenesis / negative regulation of cell motility / VEGFA-VEGFR2 Pathway / regulation of T cell differentiation in thymus / protein localization to membrane / GTPase complex / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / blood vessel morphogenesis / cellular response to insulin-like growth factor stimulus / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of epidermal growth factor receptor signaling pathway / small GTPase-mediated signal transduction / epidermal growth factor receptor binding / establishment of cell polarity / regulation of GTPase activity / enzyme-linked receptor protein signaling pathway / regulation of T cell proliferation / roof of mouth development / ERBB2-ERBB3 signaling pathway / dendrite development / positive regulation of smooth muscle cell migration / eyelid development in camera-type eye / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / neurotrophin TRK receptor signaling pathway / B cell homeostasis / hair follicle development / cellular response to nitric oxide / ephrin receptor signaling pathway / regulation of signal transduction
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Histone-fold / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PHENYLETHANE / Son of sevenless homolog 1 / Adapter molecule crk
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNguyen, J.T. / Turck, C.W. / Cohen, F.E. / Zuckermann, R.N. / Lim, W.A.
CitationJournal: Science / Year: 1998
Title: Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors.
Authors: Nguyen, J.T. / Turck, C.W. / Cohen, F.E. / Zuckermann, R.N. / Lim, W.A.
History
DepositionNov 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2013Group: Non-polymer description
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PROTO-ONCOGENE CRK (CRK))
C: PROTEIN (SH3 PEPTOID INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3193
Polymers9,2132
Non-polymers1061
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area4710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.800, 36.800, 52.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein PROTEIN (PROTO-ONCOGENE CRK (CRK)) / P38 / ADAPTER MOLECULE CRK


Mass: 7787.548 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q64010
#2: Protein/peptide PROTEIN (SH3 PEPTOID INHIBITOR)


Mass: 1425.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: Q62245*PLUS
#3: Chemical ChemComp-PYJ / PHENYLETHANE / Ethylbenzene


Mass: 106.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growpH: 6
Details: 29% PEG4000, 0.2 M AMMONIUM ACETATE, PH 6.0, pH 6.00
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
129 %PEG400011
20.2 Mammonium acetate11

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15685 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.062
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8 % / Rsym value: 0.075 / % possible all: 81.8
Reflection
*PLUS
Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 81.8 % / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CKB

1ckb


Resolution: 2.5→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.354 229 10.1 %
Rwork0.242 --
obs0.242 2277 92 %
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms561 0 8 46 615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.14
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.484 30 9.8 %
Rwork0.317 276 -

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