[English] 日本語
Yorodumi- PDB-1cly: IGG FAB (HUMAN IGG1, KAPPA) CHIMERIC FRAGMENT (CBR96) COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cly | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | IGG FAB (HUMAN IGG1, KAPPA) CHIMERIC FRAGMENT (CBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER | |||||||||
Components | (IGG FAB (HUMAN IGG1, KAPPA)) x 2 | |||||||||
Keywords | IMMUNOGLOBULIN / IMMUNOGLOBULIN C REGION / GLYCOPROTEIN / ANTIB | |||||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / IgG immunoglobulin complex / 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 / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | |||||||||
Authors | Sheriff, S. / Bajorath, J. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 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: Journal: J.Mol.Biol. / Year: 1994 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1cly.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1cly.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 1cly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/1cly ftp://data.pdbj.org/pub/pdb/validation_reports/cl/1cly | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) 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 |
---|---|
#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.) Homo sapiens (human) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→8 Å / Cross valid method: EX POST FACTO / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|