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- PDB-2dkp: Solution structure of the PH domain of pleckstrin homology domain... -

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Basic information

Entry
Database: PDB / ID: 2dkp
TitleSolution structure of the PH domain of pleckstrin homology domain-containing protein family A member 5 from human
ComponentsPleckstrin homology domain-containing family A member 5
KeywordsSIGNALING PROTEIN / PH domain / Pleckstrin homology domain-containing protein family A member 5 / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


reproductive system development / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / Synthesis of PIPs at the plasma membrane / postsynaptic density / glutamatergic synapse / nucleoplasm / membrane / cytosol
Similarity search - Function
PKHA4-7, PH domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PH-domain like / PH domain ...PKHA4-7, PH domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Pleckstrin homology domain-containing family A member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PH domain of pleckstrin homology domain-containing protein family A member 5 from human
Authors: Li, H. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 13, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleckstrin homology domain-containing family A member 5


Theoretical massNumber of molelcules
Total (without water)14,5991
Polymers14,5991
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 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Pleckstrin homology domain-containing family A member 5 / Phosphoinositol 3-phosphate-binding protein 2 / PEPP-2


Mass: 14598.751 Da / Num. of mol.: 1 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PLEKHA5, KIAA1686, PEPP2 / Plasmid: P051025-03 / Production host: Cell free synthesis / References: UniProt: Q9HAU0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.14mM PH domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.932Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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