Primary Citation PubMed: 11896404
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eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.
(2007) Nucleic Acids Res 35
PubMed: 17567616 | PubMedCentral: PMC1933152 | DOI: 10.1093/nar/gkm351
In this example, the binding mode of ADP with the query protein (PDB: 1atp, E chain), predicted from the binding site appearing in 1l3r in PDB (c-AMP-dependent protein kinase), is shown.
Publication Year: 2007
A chemogenomics view on protein-ligand spaces.
(2009) BMC Bioinformatics 10 Suppl 6
PubMed: 19534738 | PubMedCentral: PMC2697636 | DOI: 10.1186/1471-2105-10-S6-S13
A corresponding example of a protein outlier is the PDB entry 1L3R , chain I, which is a cAMP dependent protein kinase inhibitor.
Publication Year: 2009
A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A.
(2009) Biochemistry 48
PubMed: 19886670 | PubMedCentral: PMC2789581 | DOI: 10.1021/bi901475g
Figure 7 RMSD histograms for the Gly-rich loop residues 49 through 58 computed after aligning the structures for the product and reactant states defined in the text to the PDB structures representing ... losed (1L3R) and open (1J3H) states of PKA by the rigid core.
The final loop conformation in the product state appears intermediate between closed and open conformations defined by the crystal structures of 1L3R and 1J3H, respectively.
In particular, every time a new path was generated, reference beads were realigned to match the core Cα atoms of the 1L3R PDB structure.
PKA Response to Substrate Removal Because our reactant state was derived from the ternary complex (PDB code: 1L3R) by removing the phosphorylated substrate peptide, we have an opportunity to trace spontaneous rearrangements of key residues that were previously involved in protein−protein interactions with the substrate.
Figure 1 The depicted model of the catalytic subunit of PKA was derived from the transition state analogue structure with the PDB code 1L3R by removing AlF 3 .
Reactant state setup proceeded from the crystallographic structure of the transition state analogue, PDB code: 1L3R, by removing AlF 3 and the phosphorylated substrate peptide.
In the reactant, with the nucleotide and two Mg 2+ ions bound, their conformations are similar to those in the crystal structure with PDB code 1L3R.
Allosteric regulation of glycogen synthase kinase 3?: a theoretical study.
(2010) Biochemistry 49
PubMed: 21105670 | PubMedCentral: PMC3005830 | DOI: null
The cross-correlation map of a substrate bound at the ABS exhibits high similarity to the cross-correlation map published by Cheng et al. ( 30 ), who analyzed the motions of cAMP-dependent protein kin... se (PKA) in complex with a small peptide inhibitor (PDB code 1L3R ) ( 56 ).
Publication Year: 2010
Structure of ERK2 bound to PEA-15 reveals a mechanism for rapid release of activated MAPK.
(2013) Nat Commun 4
PubMed: 23575685 | PubMedCentral: PMC3640864 | DOI: 10.1038/ncomms2687
The position of a putative peptide substrate (black; depicting residues P–3 to P+3 of a substrate from a cAPK-substrate complex/PDB:1L3R) is also depicted.
Publication Year: 2013
Unique kinase catalytic mechanism of AceK with a single magnesium ion.
(2013) PLoS One 8
PubMed: 23977203 | PubMedCentral: PMC3747045 | DOI: 10.1371/journal.pone.0072048
Comparing the AceK-ICDH complex structure with the two PKA-ligand complexed structures(PDB codes: 1L3R and 1ATP)  ,  , the active-site residues have a similar structure “primed”... for the catalyzing process.
Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6.
(2014) Elife 3
PubMed: 24642411 | PubMedCentral: PMC3953950 | DOI: 10.7554/eLife.01998
Superposition of the GSK-3/LRP6 c-motif structure with the ( A ) PKA:PKI peptide (PDB 1L3R); ( B ) CDK2:p107 peptide (PDB 1QMZ); ( C ) AKT:GSK-3 peptide (PDB 3CQU); and ( D ) DYRK:consensus peptide (P... B 2WO6) substrate complexes.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
Also, there are two metal ions captured in several crystal structures of catalytic subunit of cAMP-dependent kinase (PKAc), including the reactant, PKAc/ATP/2MG complex (PDB code 4IAC [ 49 ]), the pro... uct, PKAc/ADP/2MG complex (PDB code 4IAD, 4IAF [ 49 ]), and the transition state analog, PKAc/ADP/AlF 3 /substrate peptide/2MG complex (PDB code 1L3R [ 56 ]).
(A) PKAc/ADP/AlF 3 /substrate peptide/2MG complex (PDB code 1L3R), (B) MD snapshot of System 5, (C) the alignment of MD snapshot of System 5 with PKAc transition state analog.
Publication Year: 2015
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