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- PDB-1cly: IGG FAB (HUMAN IGG1, KAPPA) CHIMERIC FRAGMENT (CBR96) COMPLEXED W... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cly | |||||||||
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Title | IGG FAB (HUMAN IGG1, KAPPA) CHIMERIC FRAGMENT (CBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER | |||||||||
![]() | (IGG FAB (HUMAN IGG1, KAPPA)) x 2 | |||||||||
![]() | IMMUNOGLOBULIN / IMMUNOGLOBULIN C REGION / GLYCOPROTEIN / ANTIB | |||||||||
Function / homology | ![]() IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Sheriff, S. / Bajorath, J. | |||||||||
![]() | ![]() Title: The x-ray structure of an anti-tumour antibody in complex with antigen. Authors: Jeffrey, P.D. / Bajorath, J. / Chang, C.Y. / Yelton, D. / Hellstrom, I. / Hellstrom, K.E. / Sheriff, S. #1: ![]() Title: Crystallization and Preliminary X-Ray Analysis of the Monoclonal Anti-Tumor Antibody Br96 and its Complex with the Lewis Y Determinant Authors: Chang, C.Y. / Jeffrey, P.D. / Bajorath, J. / Hellstrom, I. / Hellstrom, K.E. / Sheriff, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.9 KB | Display | ![]() |
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PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 902.8 KB | Display | ![]() |
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Full document | ![]() | 917.4 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 24077.883 Da / Num. of mol.: 1 / Fragment: CHIMERIC FRAGMENT (BR96) Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER / Source: (gene. exp.) ![]() Description: HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH P2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION Fragment: CH1, IGG1 / References: UniProt: P01834*PLUS |
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#2: Antibody | Mass: 23609.449 Da / Num. of mol.: 1 / Fragment: CHIMERIC FRAGMENT (BR96) Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER / Source: (gene. exp.) ![]() Description: HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH P2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION Fragment: CH1, IGG1 |
#3: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis Y antigen / beta anomer |
#4: Chemical | ChemComp-NON / |
Sequence details | THE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN ...THE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN (RESIDUES 1 - 231) HAS BEEN ASSIGNED CHAIN INDICATOR H. THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Chang, C.Y., (1994) J.Mol.Biol., 235, 372. / pH: 4.6 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→57.8 Å / Num. obs: 20051 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.51→2.75 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2 / % possible all: 90.8 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 59769 |
Reflection shell | *PLUS % possible obs: 90.8 % |
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Processing
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Refinement | Resolution: 2.5→8 Å / Cross valid method: EX POST FACTO / σ(F): 1
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Displacement parameters | Biso mean: 47.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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