+Open data
-Basic information
Entry | Database: PDB / ID: 8quy | ||||||
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Title | Hexameric HIV-1 CA in complex with DDD01728501 | ||||||
Components | Spacer peptide 1 | ||||||
Keywords | VIRAL PROTEIN / Capsid | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Petit, A.P. / Fyfe, P.K. | ||||||
Funding support | 1items
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Citation | Journal: Chemmedchem / Year: 2024 Title: Application of an NMR/crystallography fragment screening platform for the assessment and rapid discovery of new HIV-CA binding fragments. Authors: Lang, S. / Fletcher, D.A. / Petit, A.P. / Luise, N. / Fyfe, P.K. / Zuccotto, F. / Porter, D. / Hope, A. / Bellany, F. / Kerr, C. / MacKenzie, C.J. / Wyatt, P.G. / Gray, D.W. #1: Journal: Biorxiv / Year: 2023 Title: Application of an NMR/crystallography fragment screening platform for the assessment and rapid discovery of new HIV-CA binding fragments Authors: Lang, S. / Fletcher, D.A. / Petit, A.P. / Luise, N. / Fyfe, P.K. / Zuccotto, F. / Porter, D. / Hope, D. / Bellany, F. / Kerr, C. / MacKenzie, C.J. / Wyatt, P. / Gray, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8quy.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8quy.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 8quy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/8quy ftp://data.pdbj.org/pub/pdb/validation_reports/qu/8quy | HTTPS FTP |
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-Related structure data
Related structure data | 8qubC 8quhC 8quiC 8qujC 8qukC 8qulC 8quwC 8quxC 8qv1C 8qv4C 8qv9C 8qvaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25461.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P12493 |
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#2: Chemical | ChemComp-X0L / Mass: 266.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2 / Feature type: SUBJECT OF INVESTIGATION |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→45.38 Å / Num. obs: 21682 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1069 / CC1/2: 0.52 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→45.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.188 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.399 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→45.38 Å
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Refine LS restraints |
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