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- PDB-3sem: SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 3sem
TitleSEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR
Components
  • SEX MUSCLE ABNORMAL PROTEIN 5
  • SH3 PEPTOID INHIBITOR
KeywordsSIGNALING PROTEIN/INHIBITOR / SH3 DOMAIN / INHIBITORS / PEPTOIDS / PROTEIN-PROTEIN RECOGNITION / PROLINE-RICH MOTIFS / SIGNAL TRANSDUCTION / SIGNALING PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / : / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling ...Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / : / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / PI-3K cascade:FGFR4 / RHO GTPases Activate WASPs and WAVEs / Insulin receptor signalling cascade / MET activates RAS signaling / MET activates PI3K/AKT signaling / RHOU GTPase cycle / FLT3 Signaling / PIP3 activates AKT signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR downregulation / PI3K events in ERBB2 signaling / EGFR Transactivation by Gastrin / RAF/MAP kinase cascade / Negative regulation of MET activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Cargo recognition for clathrin-mediated endocytosis / regulation of cell projection organization / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / regulation of nematode larval development / Clathrin-mediated endocytosis / regulation of vulval development / male genitalia development / COP9 signalosome / muscle organ development / epidermal growth factor receptor binding / regulation of MAPK cascade / regulation of cell migration / phosphotyrosine residue binding / epidermal growth factor receptor signaling pathway / signal transduction / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily ...Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Sex muscle abnormal protein 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 2, 1998Processing site: RCSB
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEX MUSCLE ABNORMAL PROTEIN 5
B: SEX MUSCLE ABNORMAL PROTEIN 5
C: SH3 PEPTOID INHIBITOR
D: SH3 PEPTOID INHIBITOR


Theoretical massNumber of molelcules
Total (without water)16,1784
Polymers16,1784
Non-polymers00
Water50428
1
A: SEX MUSCLE ABNORMAL PROTEIN 5
C: SH3 PEPTOID INHIBITOR


Theoretical massNumber of molelcules
Total (without water)8,0892
Polymers8,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area4370 Å2
MethodPISA
2
B: SEX MUSCLE ABNORMAL PROTEIN 5
D: SH3 PEPTOID INHIBITOR


Theoretical massNumber of molelcules
Total (without water)8,0892
Polymers8,0892
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-6 kcal/mol
Surface area4370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.050, 68.530, 35.020
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9816, 0.113, 0.1539), (0.1137, -0.9935, 0.004), (0.1534, 0.0135, -0.9881)
Vector: -10.9315, 80.6364, 84.6888)

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Components

#1: Protein SEX MUSCLE ABNORMAL PROTEIN 5


Mass: 7000.690 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SH3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29355
#2: Protein/peptide SH3 PEPTOID INHIBITOR


Mass: 1088.328 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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 Å3/Da / Density % sol: 38.49 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 50 %sat / Common name: ammonium phosphate

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 61158 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.083
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rsym value: 0.434 / % possible all: 64.2
Reflection
*PLUS
Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 64.2 % / Rmerge(I) obs: 0.434

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Processing

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

1sem


Resolution: 2.2→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.31 655 10.4 %
Rwork0.248 --
obs0.248 6292 96 %
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 28 1084
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_deg1.124
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: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.354 65 9.9 %
Rwork0.361 649 -

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