+Open data
-Basic information
Entry | Database: PDB / ID: 5f4p | ||||||
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Title | HIV-1 gp120 complex with BNM-III-170 | ||||||
Components | ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Liang, S. / Hendrickson, W.A. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2016 Title: Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition. Authors: Melillo, B. / Liang, S. / Park, J. / Schon, A. / Courter, J.R. / LaLonde, J.M. / Wendler, D.J. / Princiotto, A.M. / Seaman, M.S. / Freire, E. / Sodroski, J. / Madani, N. / Hendrickson, W.A. / Smith, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f4p.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f4p.ent.gz | 118.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f4p_validation.pdf.gz | 1000.6 KB | Display | wwPDB validaton report |
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Full document | 5f4p_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5f4p_validation.xml.gz | 29 KB | Display | |
Data in CIF | 5f4p_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/5f4p ftp://data.pdbj.org/pub/pdb/validation_reports/f4/5f4p | HTTPS FTP |
-Related structure data
Related structure data | 5f4lC 5f4rC 5f4uC 3tgrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38796.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK 293 GnTi- cells / Production host: Homo sapiens (human) / References: UniProt: C6G099*PLUS #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % |
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Crystal grow | Temperature: 290 K / Method: evaporation / Details: PEG 1500, calcium magnesium chloride, imidazole |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.236 Å / Num. obs: 26041 / % possible obs: 99.2 % / Redundancy: 6.29 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TGR Resolution: 2.6→48.236 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.236 Å
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Refine LS restraints |
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LS refinement shell |
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