[English] 日本語
![](img/lk-miru.gif)
- PDB-6mfp: Crystal Structure of the RV305 C1-C2 specific ADCC potent antibod... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6mfp | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of the RV305 C1-C2 specific ADCC potent antibody DH677.3 Fab in complex with HIV-1 clade A/E gp120 and M48U1 | ||||||||||||
![]() |
| ||||||||||||
![]() | VIRAL PROTEIN/IMMUNE SYSTEM / ANTI-HIV-1 ENV ANTIBODY DH677.3 / CD4I ANTIBODY / ADCC / HIV-1 ENV / IMMUNE SYSTEM / RV305 VACCINE TRIAL / HIV-1 GP120 / CLADE A/E 93TH057 / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Tolbert, W.D. / Young, B. / Pazgier, M. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency. Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Tolbert, W.D. / Young, B. / Mielke, D. / Jha, S. / O'Connell, R.J. / Vasan, S. / Kim, J. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. ...Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Tolbert, W.D. / Young, B. / Mielke, D. / Jha, S. / O'Connell, R.J. / Vasan, S. / Kim, J. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. / Kaewkungwal, J. / Pitisuttithum, P. / Nitayaphan, S. / Sinangil, F. / Tartaglia, J. / Phogat, S. / Kepler, T.B. / Alam, S.M. / Wiehe, K. / Saunders, K.O. / Montefiori, D.C. / Tomaras, G.D. / Moody, M.A. / Pazgier, M. / Haynes, B.F. / Ferrari, G. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 638.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 533.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6mfjSC ![]() 3tgtS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Antibody , 2 types, 4 molecules HCLD
#3: Antibody | Mass: 24504.537 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 23265.709 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Protein / Protein/peptide / Non-polymers , 3 types, 6 molecules GANM![](data/chem/img/CL.gif)
![](data/chem/img/CL.gif)
#1: Protein | Mass: 39356.613 Da / Num. of mol.: 2 / Mutation: H375S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | #7: Chemical | |
---|
-Sugars , 2 types, 24 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
---|---|
#6: Sugar | ChemComp-NAG / |
-Details
Compound details | THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEI |
---|---|
Sequence details | Authors state that Val 42 and Pro 43 of HIV-1 gp120 core are missing from UNP A0A0M3KKW9 but are ...Authors state that Val 42 and Pro 43 of HIV-1 gp120 core are missing from UNP A0A0M3KKW9 but are part of the protein and not an expression tag |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 4000 0.1 M MES pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2018 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 30469 / % possible obs: 89.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.442 / Num. unique obs: 1547 / % possible all: 90.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3TGT, 6MFJ Resolution: 3→39.6 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 79.988 / SU ML: 0.629 / Cross valid method: THROUGHOUT / ESU R Free: 0.576 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.95 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|