Primary Citation PubMed: 19035630
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs.
(2013) PLoS Comput Biol 9
PubMed: 24367248 | PubMedCentral: PMC3868525 | DOI: 10.1371/journal.pcbi.1003395
While other local minima are present, the [Fe 4 S 4 ] 2+ (open,substrate-free) simulations sample energy wells near both the open (PDB ID: 3DNF) and closed (PDB ID: 3KE8) crystal structures along PC1 ... ut do not overlap with the latter, HMBPP-bound crystal structure.
Alignment procedures implemented in the RMSD and tRMSF calculations are performed with respect to the [Fe 3 S 4 ] + (open, substrate-free) IspH crystal structure (PDB ID: 3DNF  ), aligning to the backbone atoms of D1, as this domain is the most rigid in all simulations.
Crystal structures corresponding to [Fe 3 S 4 ] + (open, substrate-free) (white square, PDB ID: 3DNF) and [Fe 4 S 4 ] 2+ (closed, HMBPP-bound) IspH (white diamond, PDB ID: 3KE8) are also projected onto PC space  ,  .
Since we want our PCA to assess how well the different simulations sample conformational space with respect to the [Fe 3 S 4 ] + (open, substrate-free) and [Fe 4 S 4 ] 2+ (closed, HMBPP-bound) IspH crystal structures (PDB ID: 3DNF and 3KE8, respectively), we first align the two crystal structures using the STructural Alignment of Multiple Proteins (STAMP) procedure  , as implemented in the VMD MultiSeq plugin  ,  .
Methods Ligand parameterization for molecular dynamics simulation Since the questions under consideration in this study begin with open, substrate-free IspH protein, we use the [Fe 3 S 4 ] + (open, substrate-free) IspH crystal structure from Rekittke, et al (PDB ID: 3DNF) as a starting point  .
The A. aeolicus [Fe 3 S 4 ] + IspH structure (PDB ID: 3DNF; henceforth referred to as [Fe 3 S 4 ] + (open, substrate-free) IspH) assumes an open conformation, with a 10×20 Å cavity where the HMBPP molecule is expected to bind at the cluster  .
Publication Year: 2013
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.