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Yorodumi- PDB-5wb9: Crystal structure of CD4 binding site antibody N60P23 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wb9 | ||||||
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Title | Crystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E strain 93TH057 gp120 core | ||||||
Components |
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Keywords | VIRAL PROTEIN / CD4 binding site / gp120 core | ||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / clade A/E 93TH057 HIV-1 gp120 core Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Gohain, N. / Tolbert, W. / Pazgier, M. | ||||||
Citation | Journal: Cell / Year: 2018 Title: Identification of Near-Pan-neutralizing Antibodies against HIV-1 by Deconvolution of Plasma Humoral Responses. Authors: Sajadi, M.M. / Dashti, A. / Rikhtegaran Tehrani, Z. / Tolbert, W.D. / Seaman, M.S. / Ouyang, X. / Gohain, N. / Pazgier, M. / Kim, D. / Cavet, G. / Yared, J. / Redfield, R.R. / Lewis, G.K. / DeVico, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wb9.cif.gz | 319.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wb9.ent.gz | 258.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/5wb9 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/5wb9 | HTTPS FTP |
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-Related structure data
Related structure data | 6bckC 3ngbS S: Starting model for refinement C: citing same article (ref.) |
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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
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24573.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23011.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 9 molecules G
#1: Protein | Mass: 39160.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 224 molecules
#5: Chemical | ChemComp-MPD / ( |
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#6: Chemical | ChemComp-MPO / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M MOPS pH 7.5, ).1M Magnesium acetate hexahydrate PH range: 6.5-7.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 2016 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 38617 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.38→2.43 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.2 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NGB Resolution: 2.4→37.33 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 20.788 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.972 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→37.33 Å
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Refine LS restraints |
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