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Yorodumi- PDB-8f9z: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f9z | ||||||
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Title | Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-14204, an HIV-1 gp120 antagonist | ||||||
Components | HIV-1 gp120 core | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / HIV-1 / NBD-14204 / small molecules / CD4-gp120 binding inhibitor / antagonist / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Chem-XKW / HIV-1 gp120 core Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Kwon, Y.D. / Kwong, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists. Authors: Curreli, F. / Kwon, Y.D. / Nicolau, I. / Burgos, G. / Altieri, A. / Kurkin, A.V. / Verardi, R. / Kwong, P.D. / Debnath, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f9z.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f9z.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 8f9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/8f9z ftp://data.pdbj.org/pub/pdb/validation_reports/f9/8f9z | HTTPS FTP |
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-Related structure data
Related structure data | 8fa0C 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: 39160.367 Da / Num. of mol.: 1 / Mutation: V1/V2, V3 deletion, H375S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: clade A/E 93TH057 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW8 | ||||||||
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#2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-XKW / ( | #4: Chemical | ChemComp-EPE / | #5: 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: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 12-14% PEG3350, 5% isopropanol, 0.1M HEPES, 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 29019 / % possible obs: 92.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.095 / Χ2: 0.072 / Net I/σ(I): 6.9 / Num. measured all: 123759 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→36.44 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→36.44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.0942 Å / Origin y: -11.0172 Å / Origin z: 14.9023 Å
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Refinement TLS group | Selection details: chain A and resi 44 through 353 |