Primary Citation PubMed: 16765986
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H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.
(2008) BMC Bioinformatics 9
PubMed: 18366663 | PubMedCentral: PMC2323388 | DOI: 10.1186/1471-2105-9-151
These were – projected onto 2DN1 – residues 97 , 40, 57 , 93 , 131, 37, 85, 2, 39.
Publication Year: 2008
Effects of macromolecular crowding on protein conformational changes.
(2010) PLoS Comput Biol 6
PubMed: 20617196 | PubMedCentral: PMC2895631 | DOI: 10.1371/journal.pcbi.1000833
Protein Organism Subcellular location Biological Function PDB code AdK Escherichia coli cytoplasm ATP-AMP transphosphorylase 4AKE & 1AKE yPDI Saccharomyces cerevisiae lumen of endoplasmic reti... ulum catalyses rearrangement of protein disulfide bonds 3BOA & 2B5E ODCase Saccharomyces cerevisiae cytoplasm converts orotidine mono- phosphate to uridine mono-phosphate, the last step in biosynthesis of pyrimidine nucleotides 1DQW & 1DQX TrpR Escherichia coli cytoplasm regulates transcription in tryptophan biosynthesis 1WRP & 3WRP Hb Homo sapiens cytoplasm oxygen transport 2DN1 & 2DN2 BGT Enterobacteria phage T4 cytoplasm of host cell catalyzes transfer of glucose from uridine diphosphoglucose to hydroxymethylcytosine in DNA 1JEJ & 1JG6 Ap 4 Aase Lupinus angustifolius cytoplasm catalyses cleavage of diadenosine tetraphosphate into ATP and AMP 1F3Y & 1JKN Results/Discussion The X-ray structures of AdK in the open and closed states are shown in Figure 1 ; comparison of open and closed structures for all the seven proteins is found in Figure S1 .
Publication Year: 2010
Molecular modeling of the human hemoglobin-haptoglobin complex sheds light on the protective mechanisms of haptoglobin.
(2013) PLoS One 8
PubMed: 23638175 | PubMedCentral: PMC3637213 | DOI: 10.1371/journal.pone.0062996
Materials and Methods Preparation of protein structures The crystal structure of human Hb containing a single αβ dimer was obtained from the Protein Data Bank (accession number 2DN1) [... 9] while the homology models of haptoglobin variant 1 was obtained from the Protein Model DataBase (accession number PM0075389)  .
Publication Year: 2013
Reaction trajectory revealed by a joint analysis of protein data bank.
PubMed: 24244274 | PubMedCentral: PMC3823880 | DOI: 10.1371/journal.pone.0077141
The oxy (2DN1) and carbonmonoxy (2DN3) forms of Hb are in red.
The R state structures, as represented by the oxy (2DN1) and carbonmonoxy (2DN3) structures [ 9 ], exhibit less conformity in a group distinct from the T group and clustering much more loosely.
2DN1 A four-character alphanumerical string is a PDB entry.
Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure.
(2014) Sci Rep 4
PubMed: 24710521 | PubMedCentral: PMC3978498 | DOI: 10.1038/srep04601
Because the quaternary change is accompanied with α 1 β 1 (α 2 β 2 ) dimer rotation 3 18 , the temporal change of the intersubunit dihedral angle χ , defined by... the four centers of mass (COMs) of subunits (see Fig. 1 ), is an index of the quaternary change; −99.5 and −89.0 degrees for T and R crystal structures (PDB ID: 2DN2 and 2DN1 15 ), respectively.
Publication Year: 2014
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