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- PDB-2lsw: Structure, sulfatide-binding properties, and inhibition of platel... -

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Basic information

Entry
Database: PDB / ID: 2lsw
TitleStructure, sulfatide-binding properties, and inhibition of platelet aggregation by a Disabled-2-derived peptide
ComponentsDisabled homolog 2
KeywordsBLOOD CLOTTING / platelet aggregation inhibitor / sulfatides / dodecylphosphocholine
Function / homology
Function and homology information


leading edge cell differentiation / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / positive regulation of clathrin-dependent endocytosis / positive regulation of early endosome to late endosome transport / negative regulation of androgen receptor signaling pathway / clathrin coat assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / clathrin-coated vesicle membrane / Formation of annular gap junctions ...leading edge cell differentiation / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / positive regulation of clathrin-dependent endocytosis / positive regulation of early endosome to late endosome transport / negative regulation of androgen receptor signaling pathway / clathrin coat assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / clathrin-coated vesicle membrane / Formation of annular gap junctions / Gap junction degradation / clathrin adaptor activity / response to salt / negative regulation of protein localization to plasma membrane / response to steroid hormone / cargo receptor activity / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / SMAD binding / positive regulation of endocytosis / positive regulation of SMAD protein signal transduction / positive regulation of epithelial to mesenchymal transition / clathrin-coated pit / positive regulation of substrate adhesion-dependent cell spreading / cellular response to epidermal growth factor stimulus / transforming growth factor beta receptor signaling pathway / receptor-mediated endocytosis / negative regulation of protein binding / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / fibrillar center / Wnt signaling pathway / negative regulation of epithelial cell proliferation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / Cargo recognition for clathrin-mediated endocytosis / negative regulation of neuron projection development / Clathrin-mediated endocytosis / positive regulation of cell migration / positive regulation of protein phosphorylation / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / Disabled homolog 2-like, sulfatide-binding motifs / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / PH-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsXiao, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure, Sulfatide Binding Properties, and Inhibition of Platelet Aggregation by a Disabled-2 Protein-derived Peptide.
Authors: Xiao, S. / Charonko, J.J. / Fu, X. / Salmanzadeh, A. / Davalos, R.V. / Vlachos, P.P. / Finkielstein, C.V. / Capelluto, D.G.
History
DepositionMay 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disabled homolog 2


Theoretical massNumber of molelcules
Total (without water)4,4051
Polymers4,4051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Disabled homolog 2 / DOC-2 / Differentially-expressed protein 2


Mass: 4405.165 Da / Num. of mol.: 1 / Fragment: UniProt residues 24-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAB2, DOC2 / Plasmid: pgex-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P98082

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D HN(CA)CO
1233D HNCO
1333D HN(CA)CB
1433D CBCA(CO)NH
1513D 1H-15N NOESY
1622D 1H-1H TOCSY
1722D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 uM [U-2H] DSS, 40 mM potassium chloride, 1 mM sodium azide, 10 mM [U-99% 2H] citric, 90% H2O/10% D2O90% H2O/10% D2O
250 uM [U-2H] DSS, 40 mM potassium chloride, 1 mM sodium azide, 10 mM [U-99% 2H] citric, 90% H2O/10% D2O90% H2O/10% D2O
350 uM [U-2H] DSS, 40 mM potassium chloride, 1 mM sodium azide, 10 mM [U-99% 2H] citric, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 uMDSS-1[U-2H]1
40 mMpotassium chloride-21
1 mMsodium azide-31
10 mMcitric-4[U-99% 2H]1
50 uMDSS-5[U-2H]2
40 mMpotassium chloride-62
1 mMsodium azide-72
10 mMcitric-8[U-99% 2H]2
50 uMDSS-9[U-2H]3
40 mMpotassium chloride-103
1 mMsodium azide-113
10 mMcitric-12[U-99% 2H]3
Sample conditionspH: 5.0 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 619
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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