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PDB ID Mentions in PubMed Central Article count: 2

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PDB ID Mentions in PubMed Central

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H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis.

(2012) PLoS Pathog 8

PubMed: 23028314 | PubMedCentral: PMC3447749 | DOI: 10.1371/journal.ppat.1002914

Virus NL2631 NL2631 NL2631 Cal07 Cal07 NAI - Oseltamivir Zanamivir Oseltamivir Zanamivir PDB ID code 4B7M 4B7J 4B7N 4B7R 4B7Q Amino acid differences * V106I, I223R, N248D V106I, I223R, N248D V106I, I2... 3R, N248D - - Data Collection Wavelength (Å) 0.9173 0.9763 0.97625 0.97950 0.97630 Space group C222 1 P42 1 2 P42 1 2 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell dimensions a, b, c (Å) 118.6, 162.5, 118.9 118.6, 118.6, 67.8 118.4, 118.4, 68.4 83.4, 149.0, 166.8 82.7, 148.8, 166.6 α, β, γ (°) 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 Resolution (Å) 30.0-2.5 (2.61-2.50) 83.8-2.4 (2.55-2.42) 83.7-2.84 (3.00-2.84) 30.0-1.90 (1.99-1.90) 82.65-2.73 (2.80-2.73) R merge 14.2 (60.8) 13.0 (41.6) 15.7 (48.1) 12.5 (72.8) 20.5 (53.8) I/σI 9.3 (2.1) 11.4 (4.5) 15.3 (6.0) 13.5 (3.0) 6.1 (2.5) Completeness (%) 93.3 (92.0) 100 (100) 100 (100) 99.7 (98.0) 99.2 (99.0) Multiplicity 5.6 (4.6) 10.8 (10.5) 13.3 (13.3) 6.4 (4.8) 6.8 (6.4) Unique reflections 37388 19102 11923 163254 55091 Refinement Resolution (Å) 95.8-2.5 84-2.42 83.6-2.84 111-1.9 82.6-2.7 No.

Oseltamivir Zanamivir Virus PDB ID K M * K I (nM) k on (µM −1 s −1 ) 10 3 ×k off (s −1 ) K i (nM) k on (µM −1 s −1 ) 10 3 ×k off (s −1 ) Wild type 4B7Q/4B7R 1.0 0.23 (0.12) 3.10 (0.12) 0.75 (0.20) 0.18 (0.03) 1.31 (0.15) 0.32 (0.10) I223R 4B7M/4B7J/4B7N 2.1 11.1 (1.10) 1.04 (0.09) 11.1 (0.90) 1.65 (0.40) 0.36 (0.12) 0.78 (0.12) H275Y ND ** 2.6 145 (32) ND ND 0.53 (0.06) 1.02 (0.04) 0.76 (0.21) I223R/H275Y ND 8.1 1750 (150) ND ND 3.92 (0.15) 0.15 (0.01) 0.72 (0.24) Measurements were performed in triplicate and values in parentheses are standard deviations from the mean.

In panel A, an overlay of three pandemic neuraminidase structures is presented: I223R mutant ligand-free structure (blue, NL2631, PDB ID code 4B7M) and both wild type (green, Cal07, PDB ID code 4B7R) and I223R mutant (white, Cal07, PDB ID code 4B7J) oseltamivir complexes.

Publication Year: 2012


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4527369

Influenza virus, H1N1 PDB code 4B7R, formed the WT sequence with a His274 residue.

Computational methods System preparation The X-ray crystal structures of H1N1 and H5N1 WT and mutant neuraminidase were extracted from Protein Data Bank (PDB) codes 4B7R (WT-H1N1), 44 2HU4 (WT-H5N1), 15 and 3CL0 (H274Y mutation-H5N1) 45 complexed with oseltamivir, obtained from the Research Collaboratory for Structural Bioinformatics.

Table 1 Crystal structures of the simulated systems, PDB codes, and abbreviations Simulated system PDB code Abbreviation * H1N1 wild-type 4B7R WT H1N1 H1N1 I222K 4B7R I222K H1N1 H1N1 H274Y 4B7R H274Y H1N1 H1N1 H274Y-I222K 4B7R H274Y-I222K H1N1 H5N1 wild-type 2HU4 WT H5N1 H5N1 I222K 2HU4 I222K H5N1 H5N1 H274Y 3CL0 H274Y H5N1 H5N1 H274Y-I222K 3CL0 H274Y-I222K H5N1 Note: * These abbreviations are used throughout the text.

Publication Year: 2015