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- PDB-4dkq: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dkq | ||||||
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Title | Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228 | ||||||
![]() | clade A/E 93TH057 HIV-1 gp120 core | ||||||
![]() | VIRAL PROTEIN/INHIBITOR / HIV-1 gp120 / clade A/E / CD4 mimic / DMJ-I-228 / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() 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 / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kwon, Y.D. / LaLonde, J.M. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Mascola, J. ...Kwon, Y.D. / LaLonde, J.M. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Mascola, J. / Schon, A. / Freire, E. / Sodroski, J. / Madani, N. / Smith III, A.B. / Kwong, P.D. | ||||||
![]() | ![]() Title: Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors. Authors: Lalonde, J.M. / Kwon, Y.D. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Schon, A. / Freire, E. / Kwong, P.D. / Mascola, J.R. / ...Authors: Lalonde, J.M. / Kwon, Y.D. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Schon, A. / Freire, E. / Kwong, P.D. / Mascola, J.R. / Sodroski, J. / Madani, N. / Smith, 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 | ![]() | 156.6 KB | Display | ![]() |
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PDB format | ![]() | 122.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 715.6 KB | Display | ![]() |
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Full document | ![]() | 719.4 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dkoC ![]() 4dkpC ![]() 4dkrC ![]() 3tgtS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39160.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-EPE / | #4: Chemical | ChemComp-0LK / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 8000, 5% iso-propanol, 0.1M HEPES 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.888→50 Å / Num. all: 31547 / Num. obs: 30727 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.09 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1107 / Rsym value: 0.379 / % possible all: 72.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TGT Resolution: 1.888→46.351 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 0 / Phase error: 20.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.679 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.93 Å2 / Biso mean: 34.0177 Å2 / Biso min: 13.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.888→46.351 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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