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- PDB-9hgc: Crystal structure of human GABARAPL1 in complex with cyclic pepti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9hgc | ||||||
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Title | Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 | ||||||
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![]() | PROTEIN BINDING / autophagy-related protein / cyclic peptide / GABARAPL1 / inhibitor | ||||||
Function / homology | ![]() glycophagy / Tat protein binding / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome assembly / autophagosome maturation ...glycophagy / Tat protein binding / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome assembly / autophagosome maturation / mitophagy / autophagosome / cytoplasmic vesicle membrane / phospholipid binding / microtubule / ciliary basal body / cilium / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / endoplasmic reticulum / Golgi apparatus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilms, J.A. / Willbold, D. / Weiergraeber, O.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Accurate de novo design of high-affinity protein-binding macrocycles using deep learning. Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. ...Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. / Murray, A. / Levine, P.M. / Schneider, M. / Vasireddy, V. / Ovchinnikov, S. / Weiergraber, O.H. / Willbold, D. / Kritzer, J.A. / Mougous, J.D. / Baker, D. / DiMaio, F. / Bhardwaj, G. #1: Journal: Biorxiv / Year: 2024 Title: Accurate de novo design of high-affinity protein binding macrocycles using deep learning. Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. ...Authors: Rettie, S.A. / Juergens, D. / Adebomi, V. / Bueso, Y.F. / Zhao, Q. / Leveille, A.N. / Liu, A. / Bera, A.K. / Wilms, J.A. / Uffing, A. / Kang, A. / Brackenbrough, E. / Lamb, M. / Gerben, S.R. / Murray, A. / Levine, P.M. / Schneider, M. / Vasireddy, V. / Ovchinnikov, S. / Weiergraber, O.H. / Willbold, D. / Kritzer, J.A. / Mougous, J.D. / Baker, D. / DiMaio, F. / Bhardwaj, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.2 KB | Display | ![]() |
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PDB format | ![]() | 94.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.8 KB | Display | ![]() |
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Full document | ![]() | 477.8 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9cdtC ![]() 9cduC ![]() 9cdvC ![]() 9hgdC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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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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Unit cell |
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Components
#1: Protein | Mass: 14212.201 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1725.718 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: cyclic peptide / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection twin | Operator: -h,l,k / Fraction: 0.48 |
Reflection | Resolution: 2.52→58.42 Å / Num. obs: 24336 / % possible obs: 99.4 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rrim(I) all: 0.238 / Net I/σ(I): 10.01 |
Reflection shell | Resolution: 2.52→2.59 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 1803 / CC1/2: 0.291 / Rrim(I) all: 3.279 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→58.42 Å
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Refine LS restraints |
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LS refinement shell |
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