[English] 日本語
Yorodumi- PDB-4dkp: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dkp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-50 | ||||||
Components | clade A/E 93TH057 HIV-1 gp120 core | ||||||
Keywords | VIRAL PROTEIN/INHIBITOR / HIV-1 gp120 / clade A/E / CD4 mimic / AWS-I-50 / VIRAL PROTEIN-INHIBITOR complex | ||||||
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 / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7978 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dkp.cif.gz | 300.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dkp.ent.gz | 244.9 KB | Display | PDB format |
PDBx/mmJSON format | 4dkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dkp_validation.pdf.gz | 947.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4dkp_full_validation.pdf.gz | 962 KB | Display | |
Data in XML | 4dkp_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 4dkp_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/4dkp ftp://data.pdbj.org/pub/pdb/validation_reports/dk/4dkp | HTTPS FTP |
-Related structure data
Related structure data | 4dkoC 4dkqC 4dkrC 3tgtS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39160.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: clade A/E 93TH057 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.06 % |
---|---|
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 source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
---|---|
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: 1.7978→50 Å / Num. all: 76573 / Num. obs: 74276 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Rsym value: 0.063 / Net I/σ(I): 17.44 |
Reflection shell | Resolution: 1.7978→1.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.18 / Rsym value: 0.598 / % possible all: 72.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TGT Resolution: 1.7978→33.705 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.315 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7978→33.705 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|