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Yorodumi- PDB-1zjd: Crystal Structure of the Catalytic Domain of Coagulation Factor X... -
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-Basic information
Entry | Database: PDB / ID: 1zjd | ||||||
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Title | Crystal Structure of the Catalytic Domain of Coagulation Factor XI in Complex with Kunitz Protease Inhibitor Domain of Protease Nexin II | ||||||
Components |
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Keywords | HYDROLASE / BLOOD CLOTTING / Coagulation Factor XI / Kunitz Protease Inhibitory Domain / Nexin II | ||||||
Function / homology | Function and homology information coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of Wnt signaling pathway / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein serine/threonine kinase binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / : / plasminogen activation / nuclear envelope lumen / suckling behavior / presynaptic active zone / dendrite development / COPII-coated ER to Golgi transport vesicle / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / ECM proteoglycans / smooth endoplasmic reticulum / Mitochondrial protein degradation / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / Intrinsic Pathway of Fibrin Clot Formation / neuron projection maintenance / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / response to interleukin-1 / positive regulation of mitotic cell cycle / extracellular matrix organization / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / platelet alpha granule lumen / locomotory behavior / positive regulation of peptidyl-threonine phosphorylation / learning / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / endosome lumen / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / positive regulation of inflammatory response / Golgi lumen / neuron cellular homeostasis / endocytosis / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / positive regulation of interleukin-6 production Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Jin, L. / Navaneetham, D. / Pandey, P. / Strickler, J.E. / Babine, R.E. / Walsh, P.N. / Abdel-Meguid, S.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural and Mutational Analyses of the Molecular Interactions between the Catalytic Domain of Factor XIa and the Kunitz Protease Inhibitor Domain of Protease Nexin 2 Authors: Navaneetham, D. / Jin, L. / Pandey, P. / Strickler, J.E. / Babine, R.E. / Abdel-Meguid, S.S. / Walsh, P.N. #1: Journal: To be Published Title: Molecular Interactions of Kunitz Protease Inhibitory Domain of Protease Nexin 2 and Catalytic Domain of Factor XIa Authors: Navaneetham, D. / Jin, L. / Babine, R.E. / Abdel-Meguid, S.S. / Walsh, P.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zjd.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zjd.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/1zjd ftp://data.pdbj.org/pub/pdb/validation_reports/zj/1zjd | HTTPS FTP |
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-Related structure data
Related structure data | 1zhmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26711.338 Da / Num. of mol.: 1 / Fragment: Catalytic Domain / Mutation: S434A, T475A, C482S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Cell line (production host): X-33 / Production host: Pichia pastoris (fungus) / References: UniProt: P03951, coagulation factor XIa |
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#2: Protein | Mass: 6276.980 Da / Num. of mol.: 1 / Fragment: Inhibitory Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1F11 / Cell line (production host): X-33 / Production host: Pichia pastoris (fungus) / References: UniProt: P05067 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.4 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop Details: Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 6, 2003 / Details: Blue Osmic Mirrors |
Radiation | Monochromator: Blue Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.22 Å / Num. all: 16847 / Num. obs: 16745 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 64.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZHM Resolution: 2.6→29.22 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 729108.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.5788 Å2 / ksol: 0.352514 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
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Xplor file |
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