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- PDB-1ncd: REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ncd | |||||||||
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Title | REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX | |||||||||
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![]() | HYDROLASE(O-GLYCOSYL) | |||||||||
Function / homology | ![]() positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / exo-alpha-(2->3)-sialidase activity ...positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / endosome to lysosome transport / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / multivesicular body / viral budding from plasma membrane / complement activation, classical pathway / antigen binding / response to bacterium / positive regulation of immune response / antibacterial humoral response / carbohydrate metabolic process / blood microparticle / host cell plasma membrane / virion membrane / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Tulip, W.R. / Varghese, J.N. / Colman, P.M. | |||||||||
![]() | ![]() Title: Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex. Authors: Tulip, W.R. / Varghese, J.N. / Laver, W.G. / Webster, R.G. / Colman, P.M. #1: ![]() Title: Crystal Structures of Two Mutant Neuraminidase-Antibody Complexes with Amino Acid Substitutions in the Interface Authors: Tulip, W.R. / Varghese, J.N. / Webster, R.G. / Laver, W.G. / Colman, P.M. #2: ![]() Title: Crystal Structures of Neuraminidase-Antibody Complexes Authors: Tulip, W.R. / Varghese, J.N. / Webster, R.G. / Air, G.M. / Laver, W.G. / Colman, P.M. #3: ![]() Title: Three-Dimensional Structure of a Complex of Antibody with Influenza Virus Neuraminidase Authors: Colman, P.M. / Laver, W.G. / Varghese, J.N. / Baker, A.T. / Tulloch, P.A. / Air, G.M. / Webster, R.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.5 KB | Display | ![]() |
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PDB format | ![]() | 139.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 32.9 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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1 | ![]()
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO N 326, PRO N 431, PRO L 8, PRO L 95, PRO L 141, PRO H 149, PRO H 151 AND PRO H 200 ARE CIS PROLINES. 2: THE COORDINATES OF THE CALCIUM ATOM ARE NOT WELL DETERMINED. THE REFERENCE STRUCTURE FOR THE CALCIUM ATOM IS THE N9 MUTANT S370L (PDB ENTRY 2NN9). | ||||||||
Details | THE COORDINATES OF THE CARBOHYDRATE IN THE EPITOPE CAN BE GENERATED FORM THE COORDINATES OF RESIDUES C 200A-C 200F BY APPLYING THE FOLLOWING TRANSFORMATION: 0.0 1.0 0.0 83.5 -1.0 0.0 0.0 83.5 0.0 0.0 1.0 0.0 |
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Components
-Protein , 1 types, 1 molecules N
#1: Protein | Mass: 43753.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 23722.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Antibody | Mass: 23668.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 70 molecules N![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF THE FOLLOWING RESIDUES DIFFERS FROM THE CHEMICAL SEQUENCE: LYS H 46 WAS REFINED AS ...THE SEQUENCE OF THE FOLLOWING RESIDUES DIFFERS FROM THE CHEMICAL SEQUENCE: LYS H 46 WAS REFINED AS GLU THR H 87 WAS REFINED AS LYS VAL H 109 WAS REFINED AS LEU SER N 81 WAS REFINED AS ILE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.74 Å3/Da / Density % sol: 74.05 % |
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Crystal grow | *PLUS pH: 6.6 / Method: vapor diffusion, hanging drop |
Components of the solutions | *PLUS Conc.: 1.7 M / Common name: potassium phosphate |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
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Processing
Software |
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Refinement | Highest resolution: 2.9 Å Details: THE COORDINATES OF THE CALCIUM ATOM ARE NOT WELL DETERMINED. THE REFERENCE STRUCTURE FOR THE CALCIUM ATOM IS THE N9 MUTANT S370L (PDB ENTRY 2NN9)
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Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 18737 / Rfactor obs: 0.157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.6 |