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- PDB-1s5i: Fab (LNKB-2) of monoclonal antibody to Human Interleukin-2, cryst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s5i | ||||||
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Title | Fab (LNKB-2) of monoclonal antibody to Human Interleukin-2, crystal structure | ||||||
![]() | (Fab-fragment of monoclonal antibody) x 2 | ||||||
![]() | IMMUNE SYSTEM / monoclonal antibody / antigen-binding fragment / interleukin-2 / x-ray analysis | ||||||
Function / homology | ![]() Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pletnev, V.Z. / Goryacheva, E.A. / Tsygannik, I.N. / Nesmeyanov, V.A. / Pletnev, S.V. / Pangborn, W. / Duax, W. | ||||||
![]() | ![]() Title: [A new crystal form of the Fab fragment of a monoclonal antibody to human interleukin-2: the three-dimensional structure at 2.7 A resolution]. Authors: Pletnev, V.Z. / Goriacheva, E.A. / Tsygannik, I.N. / Nesmeianov, V.A. / Pletnev, S.V. / Pangborn, W. / Daux, W. #1: ![]() Title: Spatial structure of a Fab-fragment of a monoclonal antibody to human interleukin-2 in two crystalline forms at a resolution of 2.2 and 2.9 angstroms Authors: Fokin, A.V. / Afonin, P.V. / Mikhailova, I.Y. / Tsygannik, I.N. / Mareeva, T.Y. / Nesmeyanov, V.A. / Pangborn, W. / Lee, N. / Duax, W. / Siszak, E. / Pletnev, V.Z. #2: ![]() Title: Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide Authors: Afonin, P.V. / Fokin, A.V. / Tsygannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Michaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. / Pangborn, W. / Duax, W. / Pletnev, V.Z. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of this protein was not deposited into any sequence database. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.8 KB | Display | ![]() |
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PDB format | ![]() | 74.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1f8tS 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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Unit cell |
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Components
#1: Antibody | Mass: 24203.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23869.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56.76 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG-8000, ZnAc, NaN3, Na(CH3)2AsO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41.5 Å / Num. all: 14370 / Num. obs: 14370 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.32 / Num. unique all: 879 / % possible all: 88.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F8T Resolution: 2.7→41.5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Cross validation maximum likelihood simulated annealing refinement (CNS package)
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Displacement parameters | Biso mean: 38.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å / Luzzati sigma a obs: 0.55 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→41.5 Å
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Refine LS restraints |
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Xplor file |
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