[English] 日本語
Yorodumi- PDB-1d5g: SOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMAN PHOSPHATASE HPTP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d5g | ||||||
---|---|---|---|---|---|---|---|
Title | SOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMAN PHOSPHATASE HPTP1E COMPLEXED WITH A PEPTIDE | ||||||
Components |
| ||||||
Keywords | HYDROLASE / PROTEIN-PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of excitatory synapse assembly / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation ...negative regulation of excitatory synapse assembly / cellular response to toxic substance / phosphatidylinositol 3-kinase regulatory subunit binding / Interleukin-37 signaling / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of PIPs at the plasma membrane / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of protein phosphorylation / protein tyrosine phosphatase activity / fibrillar center / lamellipodium / cell body / cytoskeleton / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Kozlov, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1d5g.cif.gz | 629.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1d5g.ent.gz | 547.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d5g ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d5g | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | 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 | Mass: 1610.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||
NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY AND 2D HOMONUCLEAR TECHNIQUES |
-Sample preparation
Details |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions |
| |||||||||||||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |