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Yorodumi- PDB-1ive: STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ive | |||||||||
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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. / Singh, S. / 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 | 1ive.cif.gz | 200.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ive.ent.gz | 166.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ive.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ive_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 1ive_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 1ive_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 1ive_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1ive ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1ive | HTTPS FTP |
-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: TYR 284 - PRO 285 OMEGA = 215.65 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO 326 3: ASP 329 - ASP 330 OMEGA = 210.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: THR 385 - PRO 386 OMEGA = 216.37 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: ARG 430 - LYS 431 OMEGA = 233.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
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 , 5 types, 8 molecules
#2: Polysaccharide | 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 | Source method: isolated from a genetically manipulated source #6: 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
#7: Chemical | #8: Chemical | |
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-Details
Nonpolymer details | THE CALCIUM, CA 470, STABILIZES A LOOP NEAR THE NEURAMINIDASE ACTIVE SITE. THE BANA108 INHIBITOR IS ...THE CALCIUM, CA 470, STABILIZES |
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Source details | MOLECULE_NAME: BANA108 SYNTHETIC. SEE SINGH ET AL. (SUBMITTED TO J. MED CHEM.) AND JEDRZEJAS ET AL. ...MOLECULE_NAME: BANA108 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: 3.52 Å3/Da / Density % sol: 65.04 % |
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Crystal grow | Details: NATIVE CRYSTALS SOAKED IN 5MM BANA108 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: 25898 / Observed criterion σ(I): 1 |
Reflection | *PLUS Rmerge(I) obs: 0.093 |
-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 BANA108 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 BANA108 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 BANA108 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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