[English] 日本語
![](img/lk-miru.gif)
- PDB-7pc3: The second PDZ domain of DLG1 complexed with the PDZ-binding moti... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7pc3 | ||||||
---|---|---|---|---|---|---|---|
Title | The second PDZ domain of DLG1 complexed with the PDZ-binding motif of HTLV1-TAX1 | ||||||
![]() |
| ||||||
![]() | PEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone | ||||||
Function / homology | ![]() regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / symbiont-mediated perturbation of host exit from mitosis / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / symbiont-mediated perturbation of host exit from mitosis / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / membrane raft organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / hard palate development / establishment of centrosome localization / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of p38MAPK cascade / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / NrCAM interactions / lateral loop / reproductive structure development / immunological synapse formation / myelin sheath adaxonal region / myelin sheath abaxonal region / peristalsis / cell projection membrane / Synaptic adhesion-like molecules / smooth muscle tissue development / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / bicellular tight junction assembly / vesicle budding from membrane / cornified envelope / positive regulation of potassium ion transport / plasma membrane protein complex / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / Trafficking of AMPA receptors / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Assembly and cell surface presentation of NMDA receptors / establishment or maintenance of epithelial cell apical/basal polarity / collagen fibril organization / amyloid precursor protein metabolic process / Dissolution of Fibrin Clot / S100 protein binding / virion binding / neurotransmitter receptor localization to postsynaptic specialization membrane / endothelial cell proliferation / lens development in camera-type eye / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / Activation of Ca-permeable Kainate Receptor / regulation of myelination / cortical actin cytoskeleton organization / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of receptor recycling / positive regulation of actin filament polymerization / Negative regulation of NMDA receptor-mediated neuronal transmission / phosphatidylserine binding / Unblocking of NMDA receptors, glutamate binding and activation / receptor clustering / positive regulation of exocytosis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / intercalated disc / basement membrane / regulation of neurogenesis / lateral plasma membrane / Smooth Muscle Contraction / potassium channel regulator activity / bicellular tight junction / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / T cell proliferation / negative regulation of T cell proliferation / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Ras activation upon Ca2+ influx through NMDA receptor / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament polymerization Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cousido-Siah, A. / Trave, G. / Gogl, G. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: A scalable strategy to solve structures of PDZ domains and their complexes. Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 188 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 146.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 456.8 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pc4C ![]() 7pc5C ![]() 7pc7C ![]() 7pc8C ![]() 7pc9C ![]() 7pcbC ![]() 7qqlC ![]() 7qqmC ![]() 7qqnC ![]() 2x7zS ![]() 5n7dS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Protein/peptide , 2 types, 2 molecules AC
#1: Protein | Mass: 46970.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1264.363 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: N-terminal biotin-ttds (trioxatridecan-succinamic acid) label Source: (synth.) ![]() |
-Non-polymers , 4 types, 406 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium sulfate, 0.1 M bis-Tris pH 5.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.553 Å / Num. obs: 36311 / % possible obs: 99.2 % / Redundancy: 13.37 % / CC1/2: 0.998 / Rrim(I) all: 0.178 / Net I/σ(I): 12.58 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 1.79 / Num. unique obs: 2616 / CC1/2: 0.645 / Rrim(I) all: 1.605 / % possible all: 98.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5N7D, 2X7Z Resolution: 1.95→46.553 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.96 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.94 Å2 / Biso mean: 30.8243 Å2 / Biso min: 11.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→46.553 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|