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- PDB-6p8m: Crystal Structure of Antibody P-p3b3 A60C Heavy Chain in Complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p8m | |||||||||
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Title | Crystal Structure of Antibody P-p3b3 A60C Heavy Chain in Complex with 426c HIV-1 gp120 core G459C | |||||||||
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Function / homology | ![]() host cell endosome membrane / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Weidle, C. / Pancera, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Overcoming Steric Restrictions of VRC01 HIV-1 Neutralizing Antibodies through Immunization. Authors: Parks, K.R. / MacCamy, A.J. / Trichka, J. / Gray, M. / Weidle, C. / Borst, A.J. / Khechaduri, A. / Takushi, B. / Agrawal, P. / Guenaga, J. / Wyatt, R.T. / Coler, R. / Seaman, M. / LaBranche, ...Authors: Parks, K.R. / MacCamy, A.J. / Trichka, J. / Gray, M. / Weidle, C. / Borst, A.J. / Khechaduri, A. / Takushi, B. / Agrawal, P. / Guenaga, J. / Wyatt, R.T. / Coler, R. / Seaman, M. / LaBranche, C. / Montefiori, D.C. / Veesler, D. / Pancera, M. / McGuire, A. / Stamatatos, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289.1 KB | Display | ![]() |
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PDB format | ![]() | 232 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6p8nC ![]() 6mftS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules C
#1: Protein | ![]() Mass: 38694.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 25374.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#3: Antibody | Mass: 23704.377 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Sugars , 2 types, 10 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 6 types, 25 molecules ![](data/chem/img/NH4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-NH4 / ![]() #7: Chemical | ![]() #8: Chemical | ![]() #9: Chemical | ChemComp-NA / #10: Chemical | ChemComp-CL / | ![]() #11: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.34 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.67% PEG 4000, 0.67M Ammonium Citrate pH 5.5 / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.59→50 Å / Num. obs: 11547 / % possible obs: 82.5 % / Redundancy: 2.8 % / CC1/2: 0.99 / Net I/σ(I): 7.75 |
Reflection shell | Resolution: 3.59→3.65 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.075 / Num. unique obs: 468 / CC1/2: 0.801 / % possible all: 75.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6MFT Resolution: 3.594→50 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.594→50 Å
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Refine LS restraints |
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LS refinement shell |
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