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Yorodumi- PDB-1e4w: crossreactive binding of a circularized peptide to an anti-TGFalp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e4w | ||||||
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Title | crossreactive binding of a circularized peptide to an anti-TGFalpha antibody Fab-fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / COMPLEX (ANTIBODY-ANTIGEN) / CROSS-REACTIVITY / PROTEIN-PEPTIDE RECOGNITION | ||||||
Function / homology | Function and homology information positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment ...positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / positive regulation of endocytosis / endosome to lysosome transport / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / multivesicular body / B cell differentiation / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular space / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hahn, M. / Winkler, D. / Misselwitz, R. / Wessner, H. / Welfle, K. / Zahn, G. / Schneider-Mergener, J. / Hoehne, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Cross-Reactive Binding of Cyclic Peptides to an Anti-Tgf Alpha Antibody Fab Fragment: An X-Ray Structural and Thermodynamic Analysis Authors: Hahn, M. / Winkler, D. / Welfle, K. / Misselwitz, R. / Welfle, H. / Wessner, H. / Zahn, G. / Scholz, C. / Seifert, M. / Harkins, R. / Schneider-Mergener, J. / Hoehne, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e4w.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e4w.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 1e4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e4w ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e4w | HTTPS FTP |
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-Related structure data
Related structure data | 1e4xC 1fbiS C: citing same article (ref.) 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
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 925.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 22884.605 Da / Num. of mol.: 1 / Fragment: IG KAPPA HEAVY CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN / References: UniProt: P01865*PLUS |
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#2: Antibody | Mass: 23577.947 Da / Num. of mol.: 1 / Fragment: IG KAPPA LIGHT CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C / References: UniProt: P01837*PLUS |
-Non-polymers , 3 types, 411 molecules
#4: Chemical | ChemComp-NI / |
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#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | CHAIN P IS A CIRCULAR CLOSED HEPTAMER OF THE SEQUENCE SER-HIS-PHE-ASN-GLU-TYR-GLU. THE N-ATOM OF ...CHAIN P IS A CIRCULAR CLOSED HEPTAMER OF THE SEQUENCE SER-HIS-PHE-ASN-GLU-TYR-GLU. THE N-ATOM OF SER-1 IS COVALENTLY |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 51.1 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN IN TRIS-HCL, 8.5 11-14 MG/ML PRECIPITANT: 12% PEG MME 2000, 5 MM NICL2, 0.1 M TRIS-HCL, PH 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.3 |
Detector | Type: XRAY RESEARCH / Detector: CCD / Date: Jun 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→74.5 Å / Num. obs: 39968 / % possible obs: 94.6 % / Redundancy: 9.9 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 5.7 / % possible all: 54.2 |
Reflection shell | *PLUS % possible obs: 54.2 % / Mean I/σ(I) obs: 6.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FBI Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 35.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.016 |