+Open data
-Basic information
Entry | Database: PDB / ID: 1seq | ||||||
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Title | Fab MNAC13 | ||||||
Components | (Monoclonal Antibody ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin | ||||||
Function / homology | Function and homology information 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 / Fc-gamma receptor I complex binding / phagocytosis, engulfment / IgG immunoglobulin complex / immunoglobulin mediated immune response / immunoglobulin complex, circulating ...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 / Fc-gamma receptor I complex binding / phagocytosis, engulfment / IgG immunoglobulin complex / 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 / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Covaceuszach, S. / Cattaneo, A. / Lamba, D. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Neutralization of NGF-TrkA Receptor Interaction by the Novel Antagonistic anti-TrkA Monoclonal Antibody MNAC13: a Structural Insight Authors: Covaceuszach, S. / Cattaneo, A. / Lamba, D. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Purification, crystallization and preliminary X-ray analysis of the Fab fragment from MNAC13, a novel antagonistic anti-tyrosine kinase A receptor monoclonal antibody Authors: Covaceuszach, S. / Cattaneo, A. / Lamba, D. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of this protein is not available in any of the database sequence. Author ...SEQUENCE The sequence of this protein is not available in any of the database sequence. Author states that Glu:L17; Glu:L18; Glu:L81; Asp:L142 are considered as Ser due to decarboxylation (radiation damage). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1seq.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1seq.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 1seq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/1seq ftp://data.pdbj.org/pub/pdb/validation_reports/se/1seq | HTTPS FTP |
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-Related structure data
Related structure data | 1bm3S S: Starting model for refinement |
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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 LH
#1: Antibody | Mass: 23107.381 Da / Num. of mol.: 1 / Fragment: FAB Light Chain / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS |
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#2: Antibody | Mass: 24030.076 Da / Num. of mol.: 1 / Fragment: FAB Heavy Chain / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868*PLUS |
-Non-polymers , 4 types, 357 molecules
#3: Chemical | ChemComp-TRS / | ||
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#4: Chemical | ChemComp-IPA / | ||
#5: Chemical | ChemComp-SO4 / #6: 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: 2.17 Å3/Da / Density % sol: 42.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 M ammonium sulfate, 5%(v/v) 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 18, 2000 / Details: Sagitally focusing Ge(220) and a multilayer |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→39 Å / Num. obs: 38392 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.063 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.78→1.83 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 1893 / Rsym value: 0.398 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BM3 Resolution: 1.78→38.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1775680.62 / Data cutoff high rms absF: 1775680.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.8362 Å2 / ksol: 0.358609 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→38.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.89 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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