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Yorodumi- PDB-1nma: N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nma | |||||||||
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Title | N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRICAL FREE-ENERGY CALCULATIONS CAPTURE SPECIFICITY TRENDS OBSERVED WITH MUTANT BINDING DATA | |||||||||
Components |
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Keywords | COMPLEX (HYDROLASE/IMMUNOGLOBULIN) / COMPLEX (HYDROLASE-IMMUNOGLOBULIN) / COMPLEX (HYDROLASE-IMMUNOGLOBULIN) complex | |||||||||
Function / homology | Function and homology information : / : / : / 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 Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | |||||||||
Authors | Tulip, W.R. / Varghese, J.N. / Colman, P.M. | |||||||||
Citation | Journal: Biochemistry / Year: 1994 Title: N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free energy calculations capture specificity trends observed with mutant binding data. Authors: Tulip, W.R. / Harley, V.R. / Webster, R.G. / Novotny, J. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Refined Crystal Structures 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. #2: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1989 Title: Three Dimensional Structures of Influenza Virus Neuraminidase-Antibody Complexes Authors: Colman, P.M. / Tulip, W.R. / Varghese, J.N. / Tulloch, P.A. / Baker, A.T. / Laver, W.G. / Air, G.M. / Webster, R.G. #3: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1989 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nma.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nma.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nma_validation.pdf.gz | 500.9 KB | Display | wwPDB validaton report |
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Full document | 1nma_full_validation.pdf.gz | 530.8 KB | Display | |
Data in XML | 1nma_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 1nma_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nma ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nma | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: GLY N 248 - PRO N 249 OMEGA = 214.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO N 326 3: ARG N 327 - PRO N 328 OMEGA = 146.03 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: CIS PROLINE - PRO N 431 / 5: CIS PROLINE - PRO L 95 | ||||||||
Details | THE COORDINATES OF THE CARBOHYDRATE 200A - 200F DO NOT REQUIRE TRANSFORMATION TO APPEAR AS PART OF THE EPITOPE. THIS CARBOHYDRATE IS COVALENTLY ATTACHED TO THE NEURAMINIDASE SUBUNIT WHICH IS NEIGHBORING TO THE ONE IN THIS FILE. |
-Components
#1: Protein | Mass: 43640.535 Da / Num. of mol.: 1 / Mutation: WILD TYPE / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / References: UniProt: P05803, exo-alpha-sialidase |
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#2: Antibody | Mass: 12129.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM MONOCLONAL MURINE ANTIBODY / Source: (natural) Mus musculus (house mouse) / References: GenBank: 501094 |
#3: Antibody | Mass: 13424.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM MONOCLONAL MURINE ANTIBODY / Source: (natural) Mus musculus (house mouse) / References: GenBank: 501094 |
#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 |
#5: Sugar | ChemComp-NAG / |
Compound details | NEURAMINIDASE RESIDUES 458 - 468 ARE INCORRECT, ALL BEING ONE RESIDUE OUT OF REGISTER. THEY ARE NOT ...NEURAMINID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 71.09 % |
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Crystal grow | *PLUS Method: unknown |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.2 / Rfactor obs: 0.2 / Highest resolution: 3 Å Details: NO SOLVENT ATOMS AND NO CALCIUM ATOM. THE REFERENCE STRUCTURE FOR THE CALCIUM ATOM IS THE N9 MUTANT S370L (PDB ENTRY 2NN9). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |