Citations in PubMed

Primary Citation PubMed: 15299527 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 47

Citations in PubMed

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PDB ID Mentions in PubMed Central

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.

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EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB).

(2007) Immunome Res 3

PubMed: 17313688 | PubMedCentral: PMC1810240 | DOI: 10.1186/1745-7580-3-3

For an average structure in the PDB [e.g., PDB: 1ATP ], MBT requires about 60 MB of RAM, and renders approximately 20–120 frames per second (video card dependent).

Publication Year: 2007


Structural and functional diversity of the microbial kinome.

(2007) PLoS Biol 5

PubMed: 17355172 | PubMedCentral: PMC1821047 | DOI: 10.1371/journal.pbio.0050017

Accession Numbers The Protein Databank ( http://www.pdb.org ) accession numbers for the structures discussed in this paper are PKA (1ATP), A. fulgidis Rio2 (1TQP), C. elegans choline kinase (INW1), Er... 2 (1GOL), Wnk1 (1T4H), and APH(3′)-IIIa (1J7L).

Six of these residues are known to be involved in ATP and substrate binding and catalysis (G52, K72, E91, D166, N171 D184; residues numbered based on PKA structure 1ATP except where otherwise noted; see Table 3 ).

Publication Year: 2007


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, c-AMP- dependent protein kinase (PDB: 1atp chain E) was used as a query, and the name of the top hit, which corresponds to the filled circle in the top right corner, is shown in the t... xt box.

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


Conservation, variability and the modeling of active protein kinases.

(2007) PLoS One 2

PubMed: 17912359 | PubMedCentral: PMC1989141 | DOI: 10.1371/journal.pone.0000982

* Kinase Full name Species PDB code Pfam domain (residues) ACK1 activated CDC42 kinase 1 H. sapiens 1U54 [46] Protein tyrosine kinase (126-385) Akt2 RAC-β serine/threon... ne-protein kinase H. sapiens 1O6K [25] Protein kinase (152-409) CDK2 cell division protein kinase 2 H. sapiens 1JST [47] Protein kinase (4-286) CK1 casein kinase I S. pombe 1CSN [48] Protein kinase (12-237) CK2 casein kinase II subunit α Z. mays 1LP4 [49] Protein kinase (34-319) DAPK death-associated protein kinase H. sapiens 1IG1 [50] Protein kinase (13-275) IRK insulin receptor tyrosine kinase H. sapiens 1IR3 [51] Protein tyrosine kinase (1023-1290) MAPK p38γ mitogen-activated protein kinase p38γ H. sapiens 1CM8 [52] Protein kinase (27-311) PhK phosphorylase kinase O. cuniculus 1PHK [53] Protein kinase (19-287) Pim-1 proto-oncogene serine/threonine-protein kinase Pim-1 H. sapiens 1XR1 [54] Protein kinase (129-381) PKA protein kinase A M. musculus 1ATP [23] Protein kinase (43-297) PknB probable serine/threonine-protein kinase PknB M. tuberculosis 1MRU [55] Protein kinase (11-273) Rio2 Rio2 serine kinase A. fulgidus 1ZAO [56] Rio1 family (105-275) Sky1P SR protein kinase S. cerevisiae 1Q97 [57] Protein kinase (158-706) † TAO2 thousand and one amino-acid protein 2 R. norvegicus 1U5R [58] Protein kinase (28-281) ChaK ‡ transient receptor potential channel kinase M. musculus 1IA9 [2] Alpha kinase (1596-1814) * The average pair-wise sequence identity between this set as computed by ClustalW using its default parameters is 17%.

Publication Year: 2007


Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.

(2008) BMC Struct Biol 8

PubMed: 18954462 | PubMedCentral: PMC2626596 | DOI: 10.1186/1472-6807-8-45

To determine the extent that conformational variability exerts on similarity searching, we conducted retrieval experiments with query surfaces binding ATP in diverse conformations: cAMP- dependent kin... se (PDB: 1atp ) protein kinase CK2 from Z. mays (PDB: 1a6o )[ 53 ], ATP:corrinoid adenosyltransferase from S. typhimurium (PDB: 1g5t )[ 54 ], PurT-encoded glycinamide ribonucleotide transformylase from E. coli (PDB: 1kj8 )[ 55 ].

Our training data is taken from querying cAMP-dependent kinase (PDB: 1atp ) ATP binding surface against the GPSS library.

SSS distances obtained by querying the ATP binding site of cAMP-dependent kinase (PDB: 1atp ) against the GPSS ligand surface library are plotted against the molecular weight of the ligand corresponding to the library surface (a).

Binding surfaces representing different ATP conformational classes: cAMP- dependent kinase (PDB: 1atp , a), protein kinase CK2 from Z. Mays (PDB: 1a6o , b), ATP:corrinoid adenosyltransferase from S. typhimurium (PDB: 1g5t , c), PurT-encoded glycinamide ribonucleotide transformylase from E. coli (PDB: 1kj8 , d).

Publication Year: 2008


Identifying critical non-catalytic residues that modulate protein kinase A activity.

(2009) PLoS One 4

PubMed: 19270744 | PubMedCentral: PMC2650257 | DOI: 10.1371/journal.pone.0004746

Structure adapted from PDB accession number 1ATP and modeled using Pymol.

Mutations are shown using PDB file 1ATP and modeled using PyMol.

The image was made using PDB file 1ATP and modeled using PyMol.

Publication Year: 2009


Correlated mutation analysis on the catalytic domains of serine/threonine protein kinases.

(2009) PLoS One 4

PubMed: 19526051 | PubMedCentral: PMC2690836 | DOI: 10.1371/journal.pone.0005913

(B) These four sites are mapped onto the 3D structure of 1ATP.

Linkages between positions in the MSA with residue numbers from a representative structure (1ATP) represent Z-scores more than 4.

Figure S8 Mapping only the highly conserved sites (A) and mapping both the highly conserved and co-evolving sites identified by SCA (B) onto the tertiary structure of PKA catalytic domain (1ATP).

Publication Year: 2009


MolLoc: a web tool for the local structural alignment of molecular surfaces.

(2009) Nucleic Acids Res 37

PubMed: 19465382 | PubMedCentral: PMC2703929 | DOI: 10.1093/nar/gkp405

In fact, the ATP binding pocket of 1atp,E is an open cavity, while the ATP binding pocket of 1atp,EI is an internal cavity.

Hence, the two surfaces are different and the optimal alignment between the ATP binding pockets of 1atp,EI (both chains) and of 1csn,A is slightly different from the optimal alignment between the ATP binding pockets of 1atp,E (only one chain) and of 1csn,A ( Figure 7 ).

The list of other structures must belong to the PDB, and the user can specify the chain(s) using the syntax pdb_id,chain(s) (e.g. 1atp, EI).

In this example, the solution of the comparison between 1atp,EI and 1csn,A contains only corresponding atoms from chain E on structure 1atp.

The surface determination routine scales linearly with the number of atoms, ranging from a few seconds for ordinary structures (e.g. 1atp, chain E) to minutes for huge macromolecular complexes (e.g. 1aei, all chains).

Side-by-side view of 1atp, chain E and 1csn, chain A.

Publication Year: 2009


On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine.

(2009) Chem Biol Drug Des 74

PubMed: 19519740 | PubMedCentral: PMC2737611 | DOI: 10.1111/j.1747-0285.2009.00832.x

Position-specific interactions The structures of 20 staurosporine–kinase complexes were superposed on the indolocarbazole moiety of staurosporine in PDB ID 1stc in order to compare them with t... e structures of 24 adenosine phosphate–kinase complexes, which were superposed on the adenine ring from ATP in PDB ID 1atp.

Publication Year: 2009


Structural diversity of the active N-terminal kinase domain of p90 ribosomal S6 kinase 2.

(2009) PLoS One 4

PubMed: 19956600 | PubMedCentral: PMC2779450 | DOI: 10.1371/journal.pone.0008044

( A ) Active PKA (PDB code 1ATP) is shown in blue.

The stereo view of the hydrophobic patch formed deep inside the N-lobe and lined by hydrophobic residues is shown for NTD RSK2 in cyan ( A ), and in blue for PKA (PDB code 1ATP) ( B ).

Publication Year: 2009


Activating mutations in TOR are in similar structures as oncogenic mutations in PI3KCalpha.

(2009) ACS Chem Biol 4

PubMed: 19902965 | PubMedCentral: PMC2796128 | DOI: 10.1021/cb900193e

In structures of PKA, adenine and the ribose are completely buried, in the most closed structure with ATP and inhibitor peptide (1ATP) and in the structure for a transition state mimic( 18 ).

Publication Year: 2009


Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families.

(2010) PLoS Comput Biol 6

PubMed: 20072606 | PubMedCentral: PMC2796266 | DOI: 10.1371/journal.pcbi.1000636

Protein kinase family We used the crystal structure of the ternary complex of a protein kinase (PDB-Id: 1ATP, [29] ) to determine the active site residues that are within 6 Å o... the substrate ATP.

Publication Year: 2010


Reciprocally coupled residues crucial for protein kinase Pak2 activity calculated by statistical coupling analysis.

(2010) PLoS One 5

PubMed: 20209159 | PubMedCentral: PMC2830475 | DOI: 10.1371/journal.pone.0009455

PDB, 1ATP.

PDB, 1ATP.

The results with Thr 197(PKA) in PKA showed a similar pattern of affected residues as Pak2, as visualized in the structure of PKA (1ATP.

The results are superimposed on the x-ray crystal structure of PKA (1ATP.

These two residues are coordinated with manganese ions in the PKA structure (1ATP.

(c) Four specific reciprocal coupling pairs for PKA were identified on the PKA structure (1ATP.

(d) PKA (green) bound to PKI (yellow) modified from 1ATP.

Publication Year: 2010


Conformational preference of ChaK1 binding peptides: a molecular dynamics study.

(2010) PMC Biophys 3

PubMed: 20180991 | PubMedCentral: PMC2831825 | DOI: 10.1186/1757-5036-3-2

The placement of the second Mg 2+ ion was accomplished by the inspection of the active site Mn 2+ ions in the published structure of the CPK cAMP-dependent kinase (PDB entry 1ATP [ 37 ]).

Publication Year: 2010


A global optimization algorithm for protein surface alignment.

(2010) BMC Bioinformatics 11

PubMed: 20920230 | PubMedCentral: PMC2957401 | DOI: 10.1186/1471-2105-11-488

We performed pairwise comparisons of the active site of the Catalytic Subunit of cAMP- dependent Protein-Kinase (pdb code 1atp, chain E) with each of the remaining proteins of the input data set.

Figure 3 shows an example superimposition of the binding sites of ligand ATP of proteins 1atp and 1hck after the computed rototraslation is applied.

Publication Year: 2010


Co-conserved features associated with cis regulation of ErbB tyrosine kinases.

(2010) PLoS One 5

PubMed: 21179209 | PubMedCentral: PMC3001462 | DOI: 10.1371/journal.pone.0014310

C) Structural location of F327 (PKA numbering) in the C-terminal tail of PKA (PDB: 1ATP [49] ).

Publication Year: 2010


Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates.

(2010) Nat Struct Mol Biol 17

PubMed: 19966800 | PubMedCentral: PMC3006182 | DOI: 10.1038/nsmb.1705

Cdk2 (PDB ID 1JST) and PKA (PDB ID 1ATP) are from structures of the kinases in activated states (including Cdk2 bound to cyclinA with activating phosphorylation of threonine).

Publication Year: 2010


PDBe: Protein Data Bank in Europe.

(2011) Nucleic Acids Res 39

PubMed: 21045060 | PubMedCentral: PMC3013808 | DOI: 10.1093/nar/gkq985

For example, Figure 2 shows the PDBprints for PDB entry 1atp ( 22 ), which immediately reveals that 1atp is a published crystal structure of a heterologously expressed mouse protein in complex with a ... igand, for which the experimental data is available.

PDBprints for PDB entry 1atp (pdbe.org/pdbprints; see text for details).

Publication Year: 2011


Pseudokinases-remnants of evolution or key allosteric regulators?

(2010) Curr Opin Struct Biol 20

PubMed: 21074407 | PubMedCentral: PMC3014569 | DOI: 10.1016/j.sbi.2010.10.001

For VRK3 and ROP2, ATP (shown as lines) bound to PKA was modelled in the VRK3 and ROP2 structures by superposition of the PKA structure (PDBID 1ATP).

(c–h) Nucleotide binding pockets and active sites of PKA (PDBID 1ATP [ 1 ], STRADα (PDBID 3GNI [ 28 •• ], ILK (PDBID 3KMW; [ 36 •• ], HER3 (PDBID 3KEX; [ 39 • ], VRK3 (PDBID 2JII; [ 40 •• ]) and ROP2 (PDBID 2W1Z; [ 44 •• ]).

Publication Year: 2010


A model of a MAPK?substrate complex in an active conformation: a computational and experimental approach.

(2011) PLoS One 6

PubMed: 21494553 | PubMedCentral: PMC3073974 | DOI: 10.1371/journal.pone.0018594

The ATP molecule is superimposed on the structure following alignment with PKA (PDB ID: 1ATP).

Publication Year: 2011


Crystal structure of inhibitor of ?B kinase ?.

(2011) Nature 472

PubMed: 21423167 | PubMedCentral: PMC3081413 | DOI: 10.1038/nature09853

c , Superposition between xIKKβ (orange and yellow) and PKA (cyan, PDB code 1ATP).

Publication Year: 2011


Binding leverage as a molecular basis for allosteric regulation.

(2011) PLoS Comput Biol 7

PubMed: 21935347 | PubMedCentral: PMC3174156 | DOI: 10.1371/journal.pcbi.1002148

To assess the significance of the particular choice of crystal structure used we also analyzed PDB entry 1atp.

Protein coordinates are taken from PDB entry 1j3h and ligand coordinates from 1atp.

Publication Year: 2011


Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping.

(2011) PLoS Comput Biol 7

PubMed: 22125489 | PubMedCentral: PMC3219626 | DOI: 10.1371/journal.pcbi.1002288

It was shown that replacement of Arg19 of the inhibitory peptide (at position P−2, experimentally shown to bind at the −2 subsite (PDB code 1ATP)) by Gly reduces the inhibition by 520-... old, while similar Arg replacement at the equivalent P−3 position (Arg18) reduces the inhibition by only 90-fold [74] .

Moreover, the PKA-PKI complex is similarly formed with [66] (PDB code 1ATP) or without [75] (PDB code 1APM) the ATP molecule, even though in the former case, the guanidino group of the P−3 Arg is hydrogen-bonded to the ATP ribose.

The N and C lobes of each isomer (gray ribbon) were superimposed independently on the structure of the PKA-PKI complex (1ATP).

(A) Viewing key residues at the −2/5 site of the PKA/PKI complex (1ATP).

Publication Year: 2011


Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps.

(2011) BMC Biol 9

PubMed: 21835011 | PubMedCentral: PMC3224579 | DOI: 10.1186/1741-7007-9-53

The kinase domain (orange) and the ligand (green) in the PDB structure 1ATP are shown.

The prediction results were evaluated against distances calculated from the crystal structure 1ATP of mouse catalytic subunit of cAMP-dependent protein kinase complexed with Mn-ATP and a peptide inhibitor [ 59 ] in PDB, and some findings in previous studies.

Publication Year: 2011


Structural basis for the regulation of protein kinase A by activation loop phosphorylation.

(2012) J Biol Chem 287

PubMed: 22334660 | PubMedCentral: PMC3340281 | DOI: 10.1074/jbc.M111.335091

A C-lobe alignment to the wild-type enzyme in its closed conformation (PDB ID code 1ATP ) shows a total 30° rotation of the β-sheet ( Fig. 2 A ).

A , stereo view of the apo wild-type C-subunit (1J3H; tan ), the closed ternary complex (1ATP; black ) with C R194A ( red ) aligned along the αE and αF helices shows the similarity of the C-lobe and the rotation of the N-lobe.

A , alignment of wild-type apo (1J3H; olive ) and ternary complex (1ATP; gray ) showing that the conformation of the C-lobe portion of the active site is independent of substrate binding.

Publication Year: 2012


Structural analysis of Staphylococcus aureus serine/threonine kinase PknB.

(2012) PLoS One 7

PubMed: 22701750 | PubMedCentral: PMC3372466 | DOI: 10.1371/journal.pone.0039136

PknB SA-KD is in an inactive conformation In order to determine whether the structure of PknB SA-KD is in an active or an inactive conformation, we have compared it with the following kinase structure... : (i) PknB of M. tuberculosis , which is the first reported structure of a bacterial STK (PDB ID: 1O6Y [23] and 1MRU [24] ; (ii) cAMP-dependent protein kinase A (PKA) in an open conformation (PDB ID: 1CTP [34] ); (iii) a closed, active PKA structure with bound ATP (PDB ID: 1ATP [35] ); and (iv) human c-Src, a tyrosine kinase in the autoinhibited conformation (PDB ID: 2SRC [36] ).

The residues of the C-spine of PKA in a closed state (PDB ID: 1ATP [35] ) are shown for comparison.

The closed PKA structure is shown in green (PDB ID: 1ATP [35] ), and the open PKA structure is shown in red (PDB ID: 1CTP [34] ).

Structure-based sequence alignment of the S. aureus PknB kinase domain with the kinase domains of B. subtilis PrkC (no structure available), M. tuberculosis PknB (PDB ID: 1MRU [24] ), murine cAMP dependent Protein Kinase A (PDB ID: 1ATP [35] ; PDB ID: 1CTP [34] ) and human tyrosine protein kinase c-Src (PDB ID: 2SRC [36] ).

It was superimposed onto the kinase structures of active PKA (grey, PDB ID: 1ATP [35] ) and inactive c-Src (purple, PDB ID: 2SRC [36] ) using C-lobe residues 100–250.

Publication Year: 2012


Anomalous dispersion analysis of inhibitor flexibility: a case study of the kinase inhibitor H-89.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68

PubMed: 22869112 | PubMedCentral: PMC3412763 | DOI: 10.1107/S1744309112028655

Overall structure   In PDB entry 3vqh the catalytic subunit α of protein kinase A appears in its usual conformation (Fig. 3 ▶ a ), similar to that in reference structures such ... s 1atp (Zheng et al. , 1993 ▶ ) and 1cdk (Bossemeyer et al. , 1993 ▶ ) and nearly identical to an earlier structure of a PKA–H-89 complex (PDB entry 1ydt ; Engh et al. , 1996 ▶ ).

Publication Year: 2012


Design principles underpinning the regulatory diversity of protein kinases.

(2012) Philos Trans R Soc Lond B Biol Sci 367

PubMed: 22889905 | PubMedCentral: PMC3415841 | DOI: 10.1098/rstb.2012.0015

The structures used for generating the alignment are: CDK (1QMZ) [ 35 ], PKA (1ATP) [ 36 ], EGFR (2GS2) [ 37 ], choK or choline kinase (2IG7), APH or aminoglycoside kinase (3R78), fruK or fructosamine... kinase (3F7W), HSK or homoserine kinase (1FWK) [ 38 ], Rio kinase (1ZP9) [ 39 ], CHAK or TRP channel kinase (1IA9) [ 40 ], PI3K or phosphoinositide kinase (3T8M) and actinK or actin–fragmin kinase (1CJA) [ 26 ].

Publication Year: 2012


Structure of the nuclear factor ?B-inducing kinase (NIK) kinase domain reveals a constitutively active conformation.

(2012) J Biol Chem 287

PubMed: 22718757 | PubMedCentral: PMC3431628 | DOI: 10.1074/jbc.M112.366658

C , ribbon diagram of the NIK kinase domain active site compared with PhK and cAMP-dependent kinase (Protein Data Bank code 1ATP ).

Publication Year: 2012


Characterization of Staphylococcus aureus EssB, an integral membrane component of the Type VII secretion system: atomic resolution crystal structure of the cytoplasmic segment.

(2013) Biochem J 449

PubMed: 23098276 | PubMedCentral: PMC3526858 | DOI: 10.1042/BJ20121209

ATP (shown as black lines) and two Mn 2+ ions (lilac spheres) were modelled by superimposition of the ATP-bound structure of protein kinase A (PDB code 1ATP).

Publication Year: 2013


Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1? and PKR.

(2012) BMC Struct Biol 12

PubMed: 23148689 | PubMedCentral: PMC3534215 | DOI: 10.1186/1472-6807-12-28

Modeling of NS5A peptide bound to human casein kinase 1α model NS5A peptide S(P)SAS has been modeled on to the structural model of ck1α which is re-generated based on the crystal struc... ure of cAMP dependent kinase [PDB id: 1ATP] [ 19 ].

Therefore, NS5A peptide S(P)SAS has been modeled on to the structural model of ck1α which was generated based on the crystal structure of cAMP dependent kinase – peptide inhibitor (PKI) complex (PDB id: 1ATP) [ 19 ].

Sequence alignment between casein kinase 1 from Schizosaccharomyces pombe and human ck1α and structure alignment of casein kinase 1 from Schizosaccharomyces pombe [PDB id: 1CSN] [ 18 ] and cAMP dependent kinase [PDB id: 1ATP] [ 19 ] is shown in the Figure 4 .

Protein structure alignment using DALI [ 36 ] between cAMP dependent kinase (1ATP) [ 19 ] and yeast casein kinase (1CSN) [ 18 ] shows that the critical residues which are highlighted in blue are topologically equivalent.

Publication Year: 2012


Phosphorylation at SerČ? in the ATP-binding site of CaČ?/calmodulin-dependent kinase II as a mechanism for switching off the kinase activity.

(2013) Biosci Rep 33

PubMed: 23289753 | PubMedCentral: PMC3566533 | DOI: 10.1042/BSR20120116

To evaluate the possible consequences of introducing an acidic group at this position, we have modelled the wt CaMKII γ C-1 isoform, its phosphorylated form and the S26D mutant based on the st... ucture of PKA (PDB entry 1ATP).

The model was built using the structure of PKA (protein kinase) (PDB entry 1ATP) as a template.

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) [21] , [22] , the active-site residues have a similar structure “primed”... for the catalyzing process.

Publication Year: 2013


Deciphering the structural basis of eukaryotic protein kinase regulation.

(2013) PLoS Biol 11

PubMed: 24143133 | PubMedCentral: PMC3797032 | DOI: 10.1371/journal.pbio.1001680

(A) A comparison of the phosphorylated (PDB ID: 1ATP) and unphosphorylated (PDB ID: 4DFY) structures of PKA showed that the H-bond between pT197 and H87 is disrupted in the unphosphorylated state and ... he two lobes move away from each other and twist.

(A) The conserved EPK structural core is shown mapped on the catalytic subunit of PKA (PDB ID: 1ATP).

The active EPK conformation (PKA; PDB ID: 1ATP) is shown for comparison (center).

(A) The 3-dimensional structure of the Shell (teal) is shown surrounding the R-spine (maroon) in PKA (PDB ID: 1ATP).

Publication Year: 2013


SCEDS: protein fragments for molecular replacement in Phaser.

(2013) Acta Crystallogr D Biol Crystallogr 69

PubMed: 24189233 | PubMedCentral: PMC3817695 | DOI: 10.1107/S0907444913021811

( e ) cAMP-dependent protein kinase, PDB entry 1atp .

  Target Target Template Template   PDB code Conformer PDB code Conformer Training set  Alcohol dehydrogenase 6adh Closed 8adh Open  Alcohol dehydrogenase 8adh Open 6adh Closed  cAMP-dependent protein kinase 1atp Open 1ctp Closed  Citrate synthase 6csc Closed 5csc Open  Diptheria toxin 1mdt Closed 1ddt Open  Diptheria toxin 1ddt Open 1mdt Closed  Glutamine-binding protein 1wdn Closed 1ggg Open  Immunoglobulin 1hil , chain B Unbound 1him , chain M Bound  Lactoferrin 1flg Closed 1flh Open  Lactoferrin 1flh Open 1flg Closed  LAO binding protein 2lao Open 1lst Closed  Maltodextrin-binding protein 1anf Closed 1omp Open  Thymine synthase 2tsc Closed 3tms Open Test set  Adenylate kinase 1ake Open 2eck Closed  Adenylate kinase 2eck Closed 1ake Open  cAMP-dependent protein kinase 1ctp Open 1atp Closed  Calmodulin, closed 1ctr Closed 1cll Open  Calmodulin, open 1cll Open 1ctr Closed  Citrate synthase 6csc Closed 5csc Open  Glutamine-binding protein 1wdn Closed 1ggg Open  Maltodextrin-binding protein 1omp Open 1anf Closed  Pyruvate phosphate dikinase 1kbr Active 2t82 Inactive  Pyruvate phosphate dikinase 2t82 Inactive 1kbr Active Table 2 R values/ R free after ten cycles of REFMAC (Murshudov et al. , 2011 ▶ ) for structures of the whole template superimposed on the target (template) and after MR with the template divided into SCEDS fragments using the value of NDOM given The conformational change for calmodulin between the closed and open forms is too large to allow the whole template in one conformation to be superimposed on the target in the other conformation.

  PDB code Modes NDOM Fragment 1 Fragment 2 Fragment 3 Fragment 4 Fragment 5 Excluded ( a ) Adenylate kinase, closed 2eck , chain B 7, 9 3 1–35, 68–124, 155–214 (CORE) 36–67 (NMP) 125–154 (LID) — — None ( b ) Adenylate kinase, open 4ake , chain A 7, 8 3 1–34, 68–117, 164–214 (CORE) 118–163 (LID) 35–67 (NMP) — — None ( c ) Calmodulin, closed 1ctr 9, 10 2 9–83 84–147 — — — 4–8 ( d ) Calmodulin, open 1cll 9, 10 2 12–72 88–147 — — — 1–11, 73–73, 81–87 ( e ) cAMP-dependent protein kinase 1atp , chain E 7, 8 2 15–35, 125–328 36–124, 222–350 — — — 329–332 ( f ) Citrate synthase 5csc , chain A 7, 8 2 1–82, 84–276, 385–433 277–291, 295–384 — — — None ( g ) Glutamine-binding protein 1ggg , chain A 8 2 5–82, 189–224 89–183 — — — 83–88, 184–188 ( h ) Maltodextrin-binding protein 1anf 7, 9 2 113–258, 319–370 8–112, 259–303 — — — 1–7 ( i ) Pyruvate phosphate dikinase 1kbl 11 4 566–828 6–243 244–380, 515–565, 829–873 381–514 — 2–5 ( j ) Pyruvate phosphate dikinase, triple mutant 2r82 7, 10 5 6–242 709–873 539–699 379–515 243–338 2–5, 340–370, 516–538, 700–708

Publication Year: 2013


Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

(2013) BMC Bioinformatics 14 Suppl 18

PubMed: 24564209 | PubMedCentral: PMC3817810 | DOI: 10.1186/1471-2105-14-S18-S3

Their data set was composed of: CAPK, 1ctp, 1atp; Bence-Jones protein, 4bjl; LAO-binding protein, 2lao, 1lst; adenylate kinase, 2ak3, 1ake; glutamine binding protein, 1ggg, 1wdn; DNA polymerase ... 2; , 2bpg, 1bpd; calmodulin, 1cfd, 1cll; inorganic pyrophosphatase, 1k23, 1k20; ribose binding protein, 1urp, 2dri; Ig domain of protein G, 1pdb; hydropterin pyrophosphokinase, 1hka; cyclophilin A, 1bck; rhizopuspepsin, 2apr, 3apr; chloramphenicol acetyltransferase, 2cla, 3cla; and proteinase A, 2sga, 5sga.

Publication Year: 2013


Structure of Aurora B-INCENP in complex with barasertib reveals a potential transinhibitory mechanism.

(2014) Acta Crystallogr F Struct Biol Commun 70

PubMed: 24598913 | PubMedCentral: PMC3944688 | DOI: 10.1107/S2053230X14002118

( d , e ) Surface representations of Aurora B with INCENP ( d ) and of protein kinase A with PKI (PDB entry 1atp ; Zheng et al. , 1993 ▶ ) ( e ).

Publication Year: 2014


Structure of cyclin G-associated kinase (GAK) trapped in different conformations using nanobodies.

(2014) Biochem J 459

PubMed: 24438162 | PubMedCentral: PMC3957475 | DOI: 10.1042/BJ20131399

Modelling of the substrate peptide (grey ribbon) and ATP-MgCl 2 (pink stick and ball) from the PKA structure (PDB code 1ATP) into GAK suggests a suitable pocket for accommodation of a substrate peptid... for phosphorylation.

Superimposition of the PKA–ATP–peptide complex (PDB code 1ATP) revealed that a docking groove created within the active site of GAK would be suitable to accommodate a peptide substrate ( Figure 3 D), which therefore suggests that this conformation of the activation segment may serve as an active conformation of the enzyme to enable peptide binding.

Publication Year: 2014


Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors.

(2014) Nat Genet 46

PubMed: 24747643 | PubMedCentral: PMC4074779 | DOI: 10.1038/ng.2956

( c ) Crystal structure of PRKACA and inhibitor (PDB: 1ATP) 9 .

Publication Year: 2014


Computational prediction of hinge axes in proteins.

(2014) BMC Bioinformatics 15 Suppl 8

PubMed: 25080829 | PubMedCentral: PMC4120148 | DOI: 10.1186/1471-2105-15-S8-S2

Protein PDB ID KINARI cutoff Pinned cluster Moving cluster Twist purity Calmodulin (calcium-free) 1CFD default 0 1 77.1269 Calmodulin (Ca 2+ -bound; open) 1CLL -2 0 1 95.435 Calmodulin (Ca2+ -bound; c... osed) 2BBM(A) default 4 7 150.339 LAO binding protein (open) 1LST default 0 1 91.5669 LAO binding protein (closed) 2LAO default 0 1 98.1407 Bence-Jones protein (open) 4BJL(B) -1.25 0 1 97.0153 Bence-Jones protein (closed) 4BJL(A) -1.25 0 1 99.0822 cAMP-dependent protein kinase (open) 1CTP -1.9 0 2 89.7223 cAMP-dependent protein kinase (closed) 1ATP -1.9 0 1 93.2537 Adenylate kinase (open) 2AK3(A) default 0 1 95.2801 Adenylate kinase (closed) 1AKE(A) -2.5 1 0 91.4916 Glutamine binding protein (open) 1GGG(A) default 1 0 105.321 Glutamine binding protein (closed) 1WDN -2 0 1 90 DNA polymerase β (open) 2BPG(A) default 0 1 109.657 DNA polymerase β (closed) 1BPD default 0 1 86.6385 Inorganic pyrophosphatase (open) 1K23(A) default 0 1 91.6584 Inorganic pyrophosphatase (closed) 1K20(A) -3 1 0 80.6779 Ribose binding protein (open) 1URP(C) -2 0 1 75.4811 Ribose binding protein (closed) 2DRI -2.65 1 0 89.4672 For structures where the PDB contains more than one chain, the analyzed chain is indicated within parentheses.

Publication Year: 2014


Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA.

(2014) PLoS One 9

PubMed: 25275314 | PubMedCentral: PMC4183626 | DOI: 10.1371/journal.pone.0109639

Materials and Methods Preparation of the Initial Structures We used the initial structure of PKA in complex with a peptide inhibitor (PDB code 1ATP; this crystal also includes ATP and Mn 2+ atoms) [12... .

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4295794

Table 2 Distances within the C-Subunit That Define Different Conformations a conformation: ADP bound (chain A/B) open intermediate closed closed closed peptide none IP20 none IP20 IP20 IP20 nucleotide... ADP none adenosine ATP none AMP-PNP PDB ID 4NTT 1CTP 1BKX 1ATP 1APM 1CDK His87–Thr197 (N-PO 4 ) 6.7/6.3 7.1 3.2 2.7 2.8 2.8 Glu170–Tyr330 (backbone C=O–OH) NA/12.3 14.6 8.6 8.2 8.2 7.9 a Adapted from Johnson et al. 2 Mg Binding Site and Implications on Reaction Progression There is only one magnesium ion present in the ADP bound structure unlike typical PKA ternary structures, which display two magnesium ions at the active site.

Publication Year: 2014


ProKinO: a unified resource for mining the cancer kinome.

(2015) Hum Mutat 36

PubMed: 25382819 | PubMedCentral: PMC4342772 | DOI: 10.1002/humu.22726

A: Phosphorylated threonine interacting with basic residues from the RD pocket (PDB:1ATP).

ATP is shown in black sticks (PDB:1ATP).

The F-helix is colored brown and adenosine triphosphate (ATP) is depicted as black sticks (PDB:1ATP).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4429360

As shown in Figure  4 , we started from a PDB entry of cAMP-dependent protein kinase < http://rdf.wwpdb.org/pdb/1ATP > (or PDBr:1ATP in short), which, after following some link... , eventually reaches UniProt entry < http://purl.uniprot.org/uniprot/P05132 > (or UP:P05132 in short).

Starting from a PDB entry PDBr:1ATP, links are followed through UniProt, PROSITE (Bio2RDF portal) to obtain other PDB entries sharing the same PROSITE motifs.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4498444

(A) Structural motifs mapped onto the ternary complex of PKA-C (Protein Data Bank entry 1ATP).

Mapping of the fractionation factors on the PKA-C structure (bottom, Protein Data Bank entry 1ATP).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4532999

This model was built by homology with the crystal structures of an abltide variant bound to an inactive form of Abl kinase 5 and of an active form of protein kinase A bound to a peptide substrate, ATP... and two magnesium ions (PDB ID: 1atp).

An initial molecular model of abltide bound to active (DFG-in) Abl kinase with an ATP molecule and two magnesium ions bound in the ATP-cleft was built by homology on the basis of three templates: the crystal structures of inactive (DFG-out) Abl kinase bound to a chemically modified abltide (PDB ID 2g2f), the crystal structure of active (DFG-in) Abl kinase bound to an ADP molecule (PDB ID 2g2i) and the crystal structure of an active cAMP kinase bound to ATP and two magnesium ions (PDB ID 1atp).

Publication Year: 2015


The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.

(2005) BMC Bioinformatics 6

PubMed: 15694009 | PubMedCentral: PMC548701 | DOI: 10.1186/1471-2105-6-21

The structure of cAMP dependant protein kinase (PDB id 1ATP) showing the hydrophilic interactions of the bound ATP to the protein and bound inhibitor which mimics substrate in the phosphotransfer reac... ion from the gamma phosphate of ATP.

Publication Year: 2005