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- PDB-2f5b: CRYSTAL STRUCTURE OF FAB' FROM THE HIV-1 NEUTRALIZING ANTIBODY 2F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f5b | ||||||
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Title | CRYSTAL STRUCTURE OF FAB' FROM THE HIV-1 NEUTRALIZING ANTIBODY 2F5 IN COMPLEX WITH ITS GP41 EPITOPE | ||||||
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![]() | IMMUNOGLOBULIN / FAB COMPLEX / HIV-1 NEUTRALIZATION / GP41 | ||||||
Function / homology | ![]() 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 / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bryson, S. / Julien, J.P. / Hynes, R.C. / Pai, E.F. | ||||||
![]() | ![]() Title: Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications. Authors: Bryson, S. / Julien, J.P. / Hynes, R.C. / Pai, E.F. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.1 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446 KB | Display | ![]() |
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Full document | ![]() | 461.3 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u8hC ![]() 1u8iC ![]() 1u8jC ![]() 1u8lC ![]() 1u8mC ![]() 1u8nC ![]() 1u8oC ![]() 1u8pC ![]() 1u8qC ![]() 1u91C ![]() 1u92C ![]() 1u93C ![]() 1u95C ![]() 2f5aC ![]() 2pw1C ![]() 2pw2C ![]() 3idgC ![]() 3idiC ![]() 3idjC ![]() 3idmC ![]() 3idnC ![]() 1clzS 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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Unit cell |
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Components
#1: Antibody | Mass: 23363.844 Da / Num. of mol.: 1 / Fragment: FAB' / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Antibody | Mass: 24955.410 Da / Num. of mol.: 1 / Fragment: FAB' / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein/peptide | Mass: 848.920 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q75760*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | pH: 6.5 Details: 1.6M AMMONIUM SULFATE, 0.1 M CITRATE PH 5.0, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SIEMENS / Detector: CCD / Date: Mar 1, 1998 / Details: QUARTZ MIRROR |
Radiation | Monochromator: SI (1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→12 Å / Num. all: 45917 / Num. obs: 39621 / % possible obs: 90 % / Redundancy: 2.8 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.035 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.313 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 1CLZ Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 882815.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 76 Å2 / ksol: 0.4113 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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