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- PDB-4nxr: Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nxr | ||||||
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Title | Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Neurexin-1 Peptide | ||||||
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![]() | signaling Protein/Peptide / Beta barrel fold protein / PDZ domain / peptide binding / specificity mutant / scaffold signaling protein for cell adhesion and cell junction / signaling domain / signaling Protein-Peptide complex | ||||||
Function / homology | ![]() positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / neuroligin family protein binding / Activated NTRK2 signals through CDK5 / neuron cell-cell adhesion / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of modification of postsynaptic actin cytoskeleton ...positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / neuroligin family protein binding / Activated NTRK2 signals through CDK5 / neuron cell-cell adhesion / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of modification of postsynaptic actin cytoskeleton / regulation of insulin secretion involved in cellular response to glucose stimulus / cell-cell contact zone / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / Neurexins and neuroligins / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / neuron projection extension / main axon / positive regulation of axonogenesis / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / CDC42 GTPase cycle / RHOA GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / axonal growth cone / positive regulation of epithelial to mesenchymal transition / cell adhesion molecule binding / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of ERK1 and ERK2 cascade / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / response to cocaine / receptor tyrosine kinase binding / kinase binding / ruffle membrane / transmembrane signaling receptor activity / G alpha (12/13) signalling events / cell-cell junction / cell migration / positive regulation of protein binding / microtubule binding / protein-containing complex assembly / microtubule / dendritic spine / membrane => GO:0016020 / positive regulation of cell migration / neuronal cell body / glutamatergic synapse / lipid binding / synapse / positive regulation of cell population proliferation / signal transduction / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, X. / Speckhard, D.C. / Shepherd, T.R. / Hengel, S.R. / Fuentes, E.J. | ||||||
![]() | ![]() Title: Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions. Authors: Liu, X. / Speckhard, D.C. / Shepherd, T.R. / Sun, Y.J. / Hengel, S.R. / Yu, L. / Fowler, C.A. / Gakhar, L. / Fuentes, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.7 KB | Display | ![]() |
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PDB format | ![]() | 23.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 727.4 KB | Display | ![]() |
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Full document | ![]() | 727.7 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nxpC ![]() 4nxqC ![]() 3kzdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10192.402 Da / Num. of mol.: 1 / Fragment: PDZ domain / Mutation: L911M, K912E, L915F, L920V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1060.158 Da / Num. of mol.: 1 / Fragment: UNP residue 659-666 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-EPE / |
#4: Chemical | ChemComp-ANS / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1M Sodium acetate, 0.1M HEPES, pH=7.5, 22% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: Dec 14, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.06 Å / Num. obs: 6821 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.035 / Mean I/σ(I) obs: 11 / % possible all: 87.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3KZD Resolution: 1.9→39.06 Å / SU ML: 0.15 / σ(F): 0.64 / Phase error: 18.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.06 Å
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Refine LS restraints |
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LS refinement shell |
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