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Open data
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Basic information
Entry | Database: PDB / ID: 8fm8 | ||||||
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Title | HIV-1 gp120 complex with CJF-IV-046 | ||||||
![]() | Envelope glycoprotein gp120 | ||||||
![]() | VIRAL PROTEIN/INHIBITOR / retrovirus / gp120 / entry inhibitor / structure-based drug design / small molecule / antiretroviral therapy / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | IMIDAZOLE / Chem-Y1T![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gong, Z. / Hendrickson, W.A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 351.9 KB | Display | ![]() |
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PDB format | ![]() | 236.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 63 KB | Display | |
Data in CIF | ![]() | 80.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8flyC ![]() 8flzC ![]() 8fm0C ![]() 8fm2C ![]() 8fm3C ![]() 8fm4C ![]() 8fm5C ![]() 8fm7C 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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1 | ![]()
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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.) ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-Y1T / ( #4: Chemical | ChemComp-IMD / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 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: 2.47→48.65 Å / Num. obs: 42968 / % possible obs: 94.3 % / Redundancy: 13.6 % / Biso Wilson estimate: 36.85 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.07 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.47→2.74 Å / Rmerge(I) obs: 1.877 / Num. unique obs: 2148 / CC1/2: 0.59 / Rpim(I) all: 0.523 |
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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: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→48.65 Å
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Refine LS restraints |
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LS refinement shell |
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