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Yorodumi- PDB-1ivc: STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ivc | |||||||||
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Title | STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE | |||||||||
Components | INFLUENZA A SUBTYPE N2 NEURAMINIDASE | |||||||||
Keywords | HYDROLASE (O-GLYCOSYL) | |||||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | |||||||||
Authors | Jedrzejas, M.J. / Luo, M. | |||||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structures of aromatic inhibitors of influenza virus neuraminidase. Authors: Jedrzejas, M.J. / Singh, S. / Brouillette, W.J. / Laver, W.G. / Air, G.M. / Luo, M. #1: Journal: To be Published Title: Structure-Based Inhibitors of Influenza Viral Neuraminidase. A Benzoic Acid Lead with Novel Interaction Authors: Singh, S. / Jedrzejas, M.J. / Air, G.M. / Luo, M. / Laver, W.G. / Brouillette, W.J. #2: Journal: To be Published Title: Benzoic Acid Inhibitors of Influenza Virus Neuraminidase Authors: Luo, M. / Jedrzejas, M.J. / Singh, S. / White, C.L. / Brouillette, W.J. / Air, G.M. / Laver, W.G. #3: Journal: J.Mol.Biol. / Year: 1991 Title: Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution Authors: Varghese, J.N. / Colman, P.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ivc.cif.gz | 200 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ivc.ent.gz | 167.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ivc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1ivc ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1ivc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 285 / 2: CIS PROLINE - PRO 326 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1),Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 82 .. 469 .. | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43141.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Tokyo/3/1967 H2N2) Strain: A/Tokyo/3/1967 H2N2 / References: UniProt: P06820, exo-alpha-sialidase |
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-Sugars , 4 types, 8 molecules
#2: 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 #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 4 molecules
#6: Chemical | #7: Chemical | |
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-Details
Nonpolymer details | THE CALCIUM, CA 470, STABILIZES A LOOP NEAR THE NEURAMINIDASE ACTIVE SITE. THE BANA106 INHIBITOR IS ...THE CALCIUM, CA 470, STABILIZES |
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Source details | MOLECULE_NAME: BANA106 SYNTHETIC. SEE SINGH ET AL. (SUBMITTED TO J. MED CHEM.) AND JEDRZEJAS ET AL. ...MOLECULE_NAME: BANA106 SYNTHETIC. SEE SINGH ET AL. (SUBMITTED TO J. MED CHEM.) AND JEDRZEJAS ET AL. (ACCEPTED BY BIOCHEMIST |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.98 % |
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Crystal grow | Details: NATIVE CRYSTALS SOAKED IN 5MM BANA106 SOLUTION, PH 6.8. |
Crystal | *PLUS Density % sol: 58 % |
Crystal grow | *PLUS Method: vapor diffusion, hanging drop |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 28488 / Observed criterion σ(I): 1 |
Reflection | *PLUS Rmerge(I) obs: 0.087 |
-Processing
Software |
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Refinement | Resolution: 2.4→6.5 Å / σ(F): 4 Details: ONLY HALF OF THE ASYMMETRIC UNIT WAS REFINED; THE REMAINING HALF WAS GENERATED USING A NONCRYSTALLOGRAPHIC TWO-FOLD AXIS. THE TOPOLOGY AND PARAMETER VALUES GENERATED FOR THE BANA106 RESIDUES ...Details: ONLY HALF OF THE ASYMMETRIC UNIT WAS REFINED; THE REMAINING HALF WAS GENERATED USING A NONCRYSTALLOGRAPHIC TWO-FOLD AXIS. THE TOPOLOGY AND PARAMETER VALUES GENERATED FOR THE BANA106 RESIDUES WERE EITHER TAKEN DIRECTLY FROM THE LITERATURE OR BY COMPARISON TO OTHER SIMILAR STRUCTURES IN THE X-PLOR TOPOLOGY AND PARAMETER LIBRARY FILES. MORE INFORMATION CONCERNING THE REFINEMENT PROTOCOLS AND BANA106 FILES IS PRESENTED IN THE ORIGINATING PAPER.
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Refinement step | Cycle: LAST / Resolution: 2.4→6.5 Å
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Refine LS restraints |
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