+Open data
-Basic information
Entry | Database: PDB / ID: 8fm0 | ||||||
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Title | HIV-1 gp120 complex with CJF-III-214 | ||||||
Components | Envelope glycoprotein gp120 | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / retrovirus / gp120 / entry inhibitor / structure-based drug design / small molecule / antiretroviral therapy / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Chem-Y1O Function and homology information | ||||||
Biological species | HIV-1 06TG.HT008 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Gong, Z. / Hendrickson, W.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Indoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity. Authors: Fritschi, C.J. / Anang, S. / Gong, Z. / Mohammadi, M. / Richard, J. / Bourassa, C. / Severino, K.T. / Richter, H. / Yang, D. / Chen, H.C. / Chiu, T.J. / Seaman, M.S. / Madani, N. / Abrams, C. ...Authors: Fritschi, C.J. / Anang, S. / Gong, Z. / Mohammadi, M. / Richard, J. / Bourassa, C. / Severino, K.T. / Richter, H. / Yang, D. / Chen, H.C. / Chiu, T.J. / Seaman, M.S. / Madani, N. / Abrams, C. / Finzi, A. / Hendrickson, W.A. / Sodroski, J.G. / Smith III, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fm0.cif.gz | 660.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fm0.ent.gz | 457.5 KB | Display | PDB format |
PDBx/mmJSON format | 8fm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fm0_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8fm0_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8fm0_validation.xml.gz | 55.9 KB | Display | |
Data in CIF | 8fm0_validation.cif.gz | 72.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/8fm0 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/8fm0 | HTTPS FTP |
-Related structure data
Related structure data | 8flyC 8flzC 8fm2C 8fm3C 8fm4C 8fm5C 8fm7C 8fm8C 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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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: 39755.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 06TG.HT008 (virus) / Production host: Homo sapiens (human) #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-Y1O / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-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: 53.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 14% to 16% (w/v) PEG 1500, 0.1 M calcium chloride, 0.1 M imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→48.79 Å / Num. obs: 501236 / % possible obs: 93.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.08→2.3 Å / Rmerge(I) obs: 1.176 / Num. unique obs: 3829 / CC1/2: 0.67 / Rpim(I) all: 0.469 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→48.79 Å / SU ML: 0.3005 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1098 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: 44.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→48.79 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: -20.281068857 Å / Origin y: 12.1363983047 Å / Origin z: -33.3630664885 Å
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Refinement TLS group | Selection details: all |