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- PDB-1dfb: STRUCTURE OF A HUMAN MONOCLONAL ANTIBODY FAB FRAGMENT AGAINST GP4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dfb | ||||||
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Title | STRUCTURE OF A HUMAN MONOCLONAL ANTIBODY FAB FRAGMENT AGAINST GP41 OF HUMAN IMMUNODEFICIENCY VIRUS TYPE I | ||||||
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![]() | IMMUNOGLOBULIN | ||||||
Function / homology | ![]() 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 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / 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 / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / 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 | ![]() | ||||||
![]() | He, X.M. / Rueker, F. / Casale, E. / Carter, D.C. | ||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.6 KB | Display | ![]() |
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PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375 KB | Display | ![]() |
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Full document | ![]() | 401 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO L 8, PRO L 139, PRO H 160, AND PRO H 162 ARE CIS PROLINES. |
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Components
#1: Antibody | Mass: 23270.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Antibody | Mass: 24443.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.04 % | ||||||||||||||||||||||||||||||
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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
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-Data collection
Radiation | Scattering type: x-ray |
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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 |
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Processing
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Refinement | Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 2.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.7 Å
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Refine LS restraints |
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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 |