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Open data
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Basic information
Entry | Database: PDB / ID: 5vla | ||||||||||||
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Title | Short PCSK9 delta-P' complex with Fusion2 peptide | ||||||||||||
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![]() | HYDROLASE / proprotein convertase / subtilisin | ||||||||||||
Function / homology | ![]() negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding ...negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / PCSK9-LDLR complex / very-low-density lipoprotein particle binding / negative regulation of receptor recycling / PCSK9-AnxA2 complex / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / signaling receptor inhibitor activity / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / very-low-density lipoprotein particle receptor binding / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / endolysosome membrane / regulation of signaling receptor activity / sodium channel inhibitor activity / lysosomal transport / low-density lipoprotein particle receptor binding / triglyceride metabolic process / COPII-coated ER to Golgi transport vesicle / apolipoprotein binding / positive regulation of receptor internalization / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / regulation of neuron apoptotic process / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / neurogenesis / liver development / kidney development / cholesterol homeostasis / Post-translational protein phosphorylation / neuron differentiation / cellular response to insulin stimulus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / : / positive regulation of neuron apoptotic process / late endosome / lysosome / early endosome / endoplasmic reticulum lumen / lysosomal membrane / serine-type endopeptidase activity / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cell surface / endoplasmic reticulum / RNA binding / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Eigenbrot, C. / Ultsch, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists. Authors: Zhang, Y. / Ultsch, M. / Skelton, N.J. / Burdick, D.J. / Beresini, M.H. / Li, W. / Kong-Beltran, M. / Peterson, A. / Quinn, J. / Chiu, C. / Wu, Y. / Shia, S. / Moran, P. / Di Lello, P. / ...Authors: Zhang, Y. / Ultsch, M. / Skelton, N.J. / Burdick, D.J. / Beresini, M.H. / Li, W. / Kong-Beltran, M. / Peterson, A. / Quinn, J. / Chiu, C. / Wu, Y. / Shia, S. / Moran, P. / Di Lello, P. / Eigenbrot, C. / Kirchhofer, D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.4 KB | Display | ![]() |
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PDB format | ![]() | 66.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.3 KB | Display | ![]() |
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Full document | ![]() | 441.6 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vl7C ![]() 5vlhC ![]() 5vlkC ![]() 5vllC ![]() 5vlpC ![]() 4nmxS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 49784.133 Da / Num. of mol.: 1 / Fragment: residues 1-452 / Mutation: R165S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||
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#2: Protein/peptide | Mass: 3556.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.35 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: calcium acetate, PEG 6000 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→26.31 Å / Num. obs: 16868 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 43.75 Å2 / Rsym value: 0.085 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.401 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NMX Resolution: 2.4→26.31 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.895 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.407 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.444 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.278
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Displacement parameters | Biso mean: 36.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→26.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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