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Open data
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Basic information
Entry | Database: PDB / ID: 7zkr | ||||||||||||
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Title | Human GABARAP in complex with stapled peptide Pen3-ortho | ||||||||||||
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![]() | PROTEIN BINDING / Autophagy-related protein / stapled peptide / GABARAP / Inhibitor | ||||||||||||
Function / homology | ![]() positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / sperm midpiece / microtubule cytoskeleton organization / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / synapse / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ueffing, A. / Brown, H. / Willbold, D. / Kritzer, J.A. / Weiergraeber, O.H. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure-Based Design of Stapled Peptides That Bind GABARAP and Inhibit Autophagy. Authors: Brown, H. / Chung, M. / Uffing, A. / Batistatou, N. / Tsang, T. / Doskocil, S. / Mao, W. / Willbold, D. / Bast Jr., R.C. / Lu, Z. / Weiergraber, O.H. / Kritzer, J.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.4 KB | Display | ![]() |
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Full document | ![]() | 460.9 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zl7C ![]() 3d32S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 14086.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1509.726 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: residues (NH2) and (OXE) are not matched although they are present in coordinate file. Please check. Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 211 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OXE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OXE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-OXE / | #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: 2.59 Å3/Da / Density % sol: 52.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: magnesium acetate, sodium cacodylate, PEG 8000 |
-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 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→70.02 Å / Num. obs: 65281 / % possible obs: 100 % / Redundancy: 17.77 % / Biso Wilson estimate: 12.02 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.132 / Net I/σ(I): 11.48 |
Reflection shell | Resolution: 1.1→1.13 Å / Mean I/σ(I) obs: 1.38 / Num. unique obs: 4816 / CC1/2: 0.559 / Rrim(I) all: 1.694 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3D32 Resolution: 1.1→49.51 Å / SU ML: 0.1115 / Cross valid method: FREE R-VALUE / Phase error: 16.8494 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→49.51 Å
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Refine LS restraints |
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LS refinement shell |
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