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- PDB-6sdb: Chimeric titin Z1Z2 functionalized with a KLER exogenous peptide ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sdb | |||||||||
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Title | Chimeric titin Z1Z2 functionalized with a KLER exogenous peptide from decorin | |||||||||
![]() | Titin,Decorin,Titin | |||||||||
![]() | STRUCTURAL PROTEIN / titin z1z2 | |||||||||
Function / homology | ![]() : / dermatan sulfate biosynthetic process / collagen type VI trimer / Chondroitin sulfate biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / Dermatan sulfate biosynthesis / extracellular matrix structural constituent conferring compression resistance / chondroitin sulfate catabolic process ...: / dermatan sulfate biosynthetic process / collagen type VI trimer / Chondroitin sulfate biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / Dermatan sulfate biosynthesis / extracellular matrix structural constituent conferring compression resistance / chondroitin sulfate catabolic process / Defective B3GALT6 causes EDSP2 and SEMDJL1 / CS/DS degradation / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / chondroitin sulfate biosynthetic process / : / A tetrasaccharide linker sequence is required for GAG synthesis / sarcomerogenesis / structural molecule activity conferring elasticity / negative regulation of vascular endothelial growth factor signaling pathway / : / telethonin binding / skeletal muscle myosin thick filament assembly / : / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / glycosaminoglycan binding / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / actinin binding / extracellular matrix binding / M band / I band / protein kinase regulator activity / cardiac muscle cell development / negative regulation of endothelial cell migration / structural constituent of muscle / sarcomere organization / positive regulation of mitochondrial depolarization / positive regulation of mitochondrial fission / skeletal muscle thin filament assembly / striated muscle thin filament / positive regulation of macroautophagy / ECM proteoglycans / positive regulation of autophagy / striated muscle contraction / muscle contraction / cardiac muscle contraction / response to mechanical stimulus / skeletal muscle tissue development / collagen binding / protein kinase A signaling / Degradation of the extracellular matrix / lysosomal lumen / negative regulation of angiogenesis / extracellular matrix organization / condensed nuclear chromosome / kidney development / positive regulation of protein secretion / animal organ morphogenesis / wound healing / placenta development / Z disc / Golgi lumen / response to calcium ion / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / collagen-containing extracellular matrix / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fleming, J.R. / Hill, C. / Mayans, O.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The ZT Biopolymer: A Self-Assembling Protein Scaffold for Stem Cell Applications. Authors: Nesterenko, Y. / Hill, C.J. / Fleming, J.R. / Murray, P. / Mayans, O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 374.3 KB | Display | ![]() |
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PDB format | ![]() | 256.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2a38S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL
NCS ensembles :
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Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 21056.512 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8WZ42, UniProt: P07585, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 216 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.77 Å3/Da / Density % sol: 78.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1 M NH4H2PO4 pH 4.6, 100 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.84 Å / Num. obs: 487636 / % possible obs: 93.8 % / Redundancy: 10.4 % / Biso Wilson estimate: 63.56 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.2779 / Rrim(I) all: 0.2799 / Net I/σ(I): 9.62 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 2.541 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 4643 / CC1/2: 0.763 / Rrim(I) all: 2.668 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2A38 Resolution: 2.8→48.84 Å / SU ML: 0.442 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 25.3778
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.84 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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