[English] 日本語
Yorodumi- PDB-1dfb: STRUCTURE OF A HUMAN MONOCLONAL ANTIBODY FAB FRAGMENT AGAINST GP4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dfb | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF A HUMAN MONOCLONAL ANTIBODY FAB FRAGMENT AGAINST GP41 OF HUMAN IMMUNODEFICIENCY VIRUS TYPE I | ||||||
Components |
| ||||||
Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / antigen binding / 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 / antibacterial humoral response / Potential therapeutics for SARS / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / 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: 2.7 Å | ||||||
Authors | He, X.M. / Rueker, F. / Casale, E. / Carter, D.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1. Authors: He, X.M. / Ruker, F. / Casale, E. / Carter, D.C. #1: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallization of the Fab from a Human Monoclonal Antibody Against Gp41 of Human Immunodeficiency Virus Type I Authors: Casale, E. / Wenisch, E. / He, X.-M. / Righetti, P.G. / Snyder, R.S. / Jungbauer, A. / Tauer, C. / Ruker, F. / Carter, D.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dfb.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dfb.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dfb_validation.pdf.gz | 375 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dfb_full_validation.pdf.gz | 401 KB | Display | |
Data in XML | 1dfb_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1dfb_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/1dfb ftp://data.pdbj.org/pub/pdb/validation_reports/df/1dfb | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUES PRO L 8, PRO L 139, PRO H 160, AND PRO H 162 ARE CIS PROLINES. |
-Components
#1: Antibody | Mass: 23270.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: GenBank: 468243, UniProt: P01834*PLUS |
---|---|
#2: Antibody | Mass: 24443.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01857 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.04 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 216.511-512 1990 / PH range low: 7.5 / PH range high: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. all: 15019 / Num. obs: 13529 / Num. measured all: 77314 / Rmerge F obs: 0.0733 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 2.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 12079 / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 4 |