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- PDB-4dvv: 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: 4dvv | ||||||
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Title | Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AS-I-261 | ||||||
![]() | clade A/E 93TH057 HIV-1 gp120 core | ||||||
![]() | viral protein/transcription inhibitor / HIV-1 gp120 / small molecule inhibitor / CD4 binding site / AS-I-261 / viral protein-transcription inhibitor complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kwon, Y.D. / Kwong, P.D. | ||||||
![]() | ![]() Title: Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site. Authors: Kwon, Y.D. / Lalonde, J.M. / Yang, Y. / Elban, M.A. / Sugawara, A. / Courter, J.R. / Jones, D.M. / Smith, A.B. / Debnath, A.K. / Kwong, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.6 KB | Display | ![]() |
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PDB format | ![]() | 246.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4dvrC ![]() 4dvsC ![]() 4dvtC ![]() 4dvwC ![]() 4dvxC ![]() 3tgtS ![]() 4dvu 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39160.367 Da / Num. of mol.: 2 / Mutation: S375H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CRYSTALLIZED SEQUENCE WAS CONSTRUCTED BY DELETION OF N-TERMINAL 1-43, BY REPLACING THE V1/V2 ...THE CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.68 % |
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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, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5 |
-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: Jun 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→26.39 Å / Num. all: 61307 / Num. obs: 58230 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 35.88 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.062 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.23 / Rsym value: 0.393 / % possible all: 63.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3TGT Resolution: 1.94→26.39 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 23.6 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.4834 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→26.39 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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