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- PDB-1d5g: SOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMAN PHOSPHATASE HPTP... -

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Basic information

Entry
Database: PDB / ID: 1d5g
TitleSOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMAN PHOSPHATASE HPTP1E COMPLEXED WITH A PEPTIDE
Components
  • HUMAN PHOSPHATASE HPTP1E
  • PEPTIDE FADSEADENEQVSAV
KeywordsHYDROLASE / PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


negative regulation of excitatory synapse assembly / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation ...negative regulation of excitatory synapse assembly / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / negative regulation of protein phosphorylation / protein dephosphorylation / non-membrane spanning protein tyrosine phosphatase activity / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / fibrillar center / lamellipodium / cell body / cytoskeleton / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / PDZ domain / Pdz3 Domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKozlov, G. / Gehring, K. / Ekiel, I.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Solution Structure of the PDZ2 Domain from Cytosolic Human Phosphatase hPTP1E Complexed with a Peptide Reveals Contribution of the beta2-beta3 Loop to PDZ Domain-Ligand Interactions
Authors: Kozlov, G. / Banville, D. / Gehring, K. / Ekiel, I.
#1: Journal: Biochemistry / Year: 2000
Title: Solution Structure of the PDZ2 Domain from Human Phosphatase hPTP1E and its Interactions with C-terminal Peptides from the Fas Receptor
Authors: Kozlov, G. / Gehring, K. / Ekiel, I.
History
DepositionOct 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: HUMAN PHOSPHATASE HPTP1E
B: PEPTIDE FADSEADENEQVSAV


Theoretical massNumber of molelcules
Total (without water)11,6312
Polymers11,6312
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HUMAN PHOSPHATASE HPTP1E


Mass: 10020.252 Da / Num. of mol.: 1 / Fragment: PDZ2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q12923
#2: Protein/peptide PEPTIDE FADSEADENEQVSAV


Mass: 1610.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
2222D NOESY
3332D NOESY
4443D 13C-SEPARATED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY AND 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

Details
Solution-IDContents
11.0-5.0 MM OF N15-LABELED PDZ2 DOMAIN WITH 20% MOLAR EXCESS OF UNLABELED PEPTIDE
21.0-5.0 MM OF UNLABELED PDZ2 DOMAIN WITH 20% MOLAR EXCESS OF UNLABELED PEPTIDE
31.0-5.0 MM OF UNLABELED PDZ2 DOMAIN WITH 20% MOLAR EXCESS OF UNLABELED PEPTIDE
41.0-5.0 MM OF DOUBLE-LABELED PDZ2 DOMAIN WITH 20% MOLAR EXCESS OF UNLABELED PEPTIDE
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.15 M NACL 6.8AMBIENT 293 K
20.15 M NACL 6.8AMBIENT 293 K
30.15 M NACL 6.8AMBIENT 293 K
40.15 M NACL 6.8AMBIENT 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1BRUKERcollection
Gifa4DELSUCprocessing
XEASY1.3.13WUTHRICHdata analysis
CNS0.5BRUNGERstructure solution
ARIA0.1NILGESstructure solution
ARIA0.1NILGESrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 1391 NON-REDUNDANT CONSTRAINTS, 1269 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 81 DIHEDRAL ANGLE RESTRAINTS, 41 HYDROGEN BOND CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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