Primary Citation PubMed: 7463482
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Positively selected sites in cetacean myoglobins contribute to protein stability.
(2013) PLoS Comput Biol 9
PubMed: 23505347 | PubMedCentral: PMC3591298 | DOI: 10.1371/journal.pcbi.1002929
The FoldX results (last two columns) are reported using two PDB structures: 1MBO and 1U7S.
Publication Year: 2013
Unfolding simulations of holomyoglobin from four mammals: identification of intermediates and ?-sheet formation from partially unfolded states.
(2013) PLoS One 8
PubMed: 24386077 | PubMedCentral: PMC3873898 | DOI: 10.1371/journal.pone.0080308
Correspondingly, the radius of gyration ( R g ) was ∼1.51 nm for sperm whale and seal Mb and ∼1.48 and 1.50 nm for pig and horse Mb, averaged from 30–35 ns, in good agreement w... th the value of 1.52 nm from the average of R g for crystal structures of sperm whale and seal Mbs (PDB IDs: 1A6M  , 1MBO  , 1U7S  , 1U7R  , and 1MBS  ).
Calculated SASA and radius of gyration ( R g ) from crystal structures were based on averages of the structures 1A6M  , 1MBO  , 1U7S  , and 1U7R  for HoloMb.
State Conditions [θ] 222 (deg cm 2 dM −1 ) f H (%) SASA (nm 2 ) R g (nm) HoloN pH 7 −23,000  ; −25,000  78 a 80.26 a 1.52 a (X-RAY); 1.8±0.2  ,  (SAXS) ApoN pH 7 −19,000±1000  53  — 1.9±0.2  (SAXS) ApoI pH 4, 0M Urea −12,000±1000  <0.41 b — 2.3±0.2  (SAXS) ApoU pH 5, 4.5M Urea −3000±1000  ∼0 — 3.4±0.2  (SAXS) a For HoloMb, average based on crystal structures 1A6M  , 1MBO  , 1U7S  , and 1U7R  .
PubMed ID is not available.
Published in 2014
Table 3 Hydrogen Bond Distances in Different Forms of Mb and DHP crystal (PDB) distance (Å) crystal (PDB) distance (Å) Met-Mb (1a6k) 2.67 Met-DHP (2qfk) 3.14/3.24 Oxy-Mb (1mbo) 2.77 Ox... -DHP (2qfn) 2.82/2.84 CO-Mb (1dwr) 3.07 CO-DHP 3.52/>10.0 Use of DFT Calculations To Estimate the Energy of Hydrogen Bonding DFT calculations were used to understand the effect of the internal and external conformations on the tautomeric state of H55.
Publication Year: 2014
The influence of selection for protein stability on dN/dS estimations.
(2014) Genome Biol Evol 6
PubMed: 25355808 | PubMedCentral: PMC4224349 | DOI: 10.1093/gbe/evu223
( C ) Posterior probabilities of per site d N /d S from M8 model (Materials and Methods) across the sequence and ( D ) mapped onto the crystal structure of sperm whale Mb (PDB code = 1MBO) ( Phillips ... 980 ).
Estimating the Effect of Point Mutations on Protein Folding Stability We used the structure of sperm whale Mb (PDB code = 1MBO) ( Phillips 1980 ) as our model protein.
To calculate the Δ G mutant , we replaced the amino acid in the PDB 1MBO and repacked and optimized the side-chains to within 10Å of the site being mutated.
Published in 2015
We transferred the coordinates of the oxygen molecule from the sperm whale oxy-Mb (PDB ID: 1MBO) [ 27 ] and constructed the horse oxy-Mb model.
Publication Year: 2015
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