Primary Citation PubMed: 8658133
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Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.
(2008) Nucleic Acids Res 36
PubMed: 18086700 | PubMedCentral: PMC2238831 | DOI: 10.1093/nar/gkm979
Following an in silico alanine scan of the substrate peptide in the crystal structure of a DnaK-substrate complex [1dkx, ( 8 )] using the FoldX force field ( 9 ), we generated a structure-based PSSM t... at reflects the individual contribution of certain substrate residue types for DnaK binding.
Publication Year: 2008
Accurate prediction of DnaK-peptide binding via homology modelling and experimental data.
(2009) PLoS Comput Biol 5
PubMed: 19696878 | PubMedCentral: PMC2717214 | DOI: 10.1371/journal.pcbi.1000475
The curves represent structures 1DKX (closed circle), 1DKY A (open square), 1DKY B (closed triangle) and 3 NMR structures from the same ensemble (open triangle, open circle, closed square).
The MCC of structure 1DKX was the highest as compared to 1DKY (A and B) and was above the MCCs of three randomly picked NMR structures from the ensemble 1Q5L ( Table 1 and Figure 3 ).
Structures of DnaK in complex with a substrate peptide were gathered from an NMR ensemble (PDB code 1Q5L)  and from different crystal structures (PDB codes 1DKX and 1DKY, of which the latter is a DnaK dimer with monomers A and B)  .
In silico b inding energy calculations using FoldX We employed FoldX version 2.7 to model mutants of the peptide bound to DnaK in the crystal structure (PDB code: 1DKX).
Publication Year: 2009
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.
(2009) BMC Bioinformatics 10 Suppl 8
PubMed: 19758473 | PubMedCentral: PMC2745591 | DOI: 10.1186/1471-2105-10-S8-S9
Following an in silico alanine scan of the substrate peptide in the crystal structure of a DnaK-substrate complex (PDBID 1DKX ) using FoldX, a structure-based PSSM that reflects the individual contrib... tion of certain substrate residue types for DnaK binding was generated.
Hsp70 chaperones: cellular functions and molecular mechanism.
(2005) Cell Mol Life Sci 62
PubMed: 15770419 | PubMedCentral: PMC2773841 | DOI: 10.1007/s00018-004-4464-6
Ribbon representation of the structure of the substrate binding domain of E. coli DnaK (PDB entry code 1DKX; [ 74 ]) with bound peptide substrate (as stick model).
X-ray structure of the β -sheet domain of E. coli DnaK (PDB entry code 1DKX; [ 74 ]) in ribbon representation in complex with the peptide NRLLLTG in stick representation.
Publication Year: 2005
Identification of regions involved in substrate binding and dimer stabilization within the central domains of yeast Hsp40 Sis1.
(2012) PLoS One 7
PubMed: 23227221 | PubMedCentral: PMC3515540 | DOI: 10.1371/journal.pone.0050927
Light blue, Sis1 CTD (PDB accession number 1C3G); red, Sis1 J-domain (PDB accession number 2O37); dark blue, Hsp70 NBD (PDB accession number 1HJO); green, DnaK SBD (PDB accession number 1DKX).
Publication Year: 2012
A structural insight into the prokaryotic heat shock transcription regulatory protein ?(32): an implication of ?(32)-DnaK interaction.
(2012) Bioinformation 8
PubMed: 23275701 | PubMedCentral: PMC3524887 | DOI: 10.6026/97320630081026
In order to build σ 32 –DnaK complex, the modeled structure of σ 32 was docked with the crystal structure of DnaK protein (PDB Code: 1DKX) using the program GRAMM [ 17 ].
Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.
(2013) Philos Trans R Soc Lond B Biol Sci 368
PubMed: 23530260 | PubMedCentral: PMC3638396 | DOI: 10.1098/rstb.2011.0410
The three-dimensional predicted full-length Ssa1p structure was modelled using R ossetta D ock protein–protein docking software ( www.rosettacommons.org ) based on the structures of bovine Hsc... 0 (1yuw) and DnaK (1dkx).
Publication Year: 2013
Hsp70 oligomerization is mediated by an interaction between the interdomain linker and the substrate-binding domain.
(2013) PLoS One 8
PubMed: 23840795 | PubMedCentral: PMC3696110 | DOI: 10.1371/journal.pone.0067961
(C) Representation of the different truncated constructs on the crystal structure of the DnaK SBD in complex with the NR peptide substrate, represented in yellow (adapted from PDB ID: 1DKX [ 8 ]).
The truncation points were designed on the basis of published structures of the homologous proteins (PDB IDs: 1DKX, 7HSC, 1UD0, 1HJO) ( Figure 1C) .
Tracking the interplay between bound peptide and the lid domain of DnaK, using molecular dynamics.
(2013) Int J Mol Sci 14
PubMed: 23774839 | PubMedCentral: PMC3709807 | DOI: 10.3390/ijms140612675
DnaK SBD Structure The coordinates of the SBD of the DnaK with a bound NR peptide, as determined by X-ray crystallography at a 2 Å resolution [ 20 ] were downloaded from the Protein Data Bank ... 36 ] (PDB ID: 1DKX).
The crystal structure of the SBD in complex with a seven-residues-long peptide; Asn 1 -Arg 2 -Leu 3 -Leu 4 -Leu 5 -Thr 6 -Gly 7 , abbreviated by NR, which was reported by Zhu et al. in 1996 (PDB ID: 1DKX) [ 20 ], was a milestone which made a great contribution to the understanding of the mechanism of recognition and specificity of Hsp70s.
In the present study we implemented molecular dynamics (MD) simulations of the SBD in a complex with the NR peptide (PDB ID: 1DKX) in order to examine the changes in the conformation of the lid once the protein is relaxed from the forces operating during the crystallization process.
List of Simulations The carried out simulations, were all based on the crystal structure of the DnaK SBD (PDB ID: 1DKX) and are detailed in Table 1 .
Simulation 3 was of the holo-complex consisting of DnaK’s SBD and the hepta-peptide as embodied in the crystal coordinates file (PDB ID: 1DKX).
For that purpose we used the crystalline SBD domain of DnaK with a bound NR peptide, (PDB ID: 1DKX) having a 2 Å resolution [ 20 ].
ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones.
(2014) PLoS Comput Biol 10
PubMed: 24831085 | PubMedCentral: PMC4022485 | DOI: 10.1371/journal.pcbi.1003624
Diagrams B and D were generated using the PDB files 1DKX  and 4B9Q  , respectively.
Publication Year: 2014
Human mitochondrial Hsp70 (mortalin): shedding light on ATPase activity, interaction with adenosine nucleotides, solution structure and domain organization.
(2015) PLoS One 10
PubMed: 25615450 | PubMedCentral: PMC4304843 | DOI: 10.1371/journal.pone.0117170
no. 1DKX) bound to a synthetic peptide in the peptide binding site [ 58 ], into the ab initio model.
Publication Year: 2015
PubMed ID is not available.
Published in 2015
In order to reproduce a correct chaperone-substrate arrangement, we took advantage of the substrate-bound X-ray structure of DnaK SBD (PDB: 1DKX Zhu et al., 1996 ).
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