Primary Citation PubMed: 10559988
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Inferring protein domain interactions from databases of interacting proteins.
(2005) Genome Biol 6
PubMed: 16207360 | PubMedCentral: PMC1257472 | DOI: 10.1186/gb-2005-6-10-r89
As another example, Cyclin N-terminal domains [Pfam:PF00134, Cyclin_N] are known from structural studies [PDB: 1QMZ ] [ 35 ] to interact with protein kinase domains [Pfam:PF00069, Pkinase].
Publication Year: 2005
Computational analyses of the surface properties of protein-protein interfaces.
(2007) Acta Crystallogr D Biol Crystallogr 63
PubMed: 17164526 | PubMedCentral: PMC2483497 | DOI: 10.1107/S0907444906046762
( a ) A molecular surface is generated from the CDK2 chain in a structure of the CDK2–cyclin A complex (PDB code 1qmz ; Brown et al. , 1999 ▶ ).
Publication Year: 2007
Binding to DNA of the RNA-polymerase II C-terminal domain allows discrimination between Cdk7 and Cdk9 phosphorylation.
(2009) Nucleic Acids Res 37
PubMed: 19136461 | PubMedCentral: PMC2651791 | DOI: 10.1093/nar/gkn1061
Cdk7/CycH complex was modeled on pCdk2/CycA structure (PDB 1QMZ) using Cdk7 and CycH structures (PDB 1UA2 and 1KXU).
CTD/DNA complex was docked into Cdk7/CycH by superimposing 5 SP 6 to the corresponding amino acids of the substrate peptide co-crystallized with pCdk2/CycA (PDB 1QMZ).
Publication Year: 2009
Insights into the conformational variability and regulation of human Nek2 kinase.
(2009) J Mol Biol 386
PubMed: 19124027 | PubMedCentral: PMC2741569 | DOI: 10.1016/j.jmb.2008.12.033
(a) Superposition of nucleotide-binding clefts of two inactive kinase conformations [Nek2-T175A ATPγS (yellow) and ATP-bound Cdk2 (cyan, Protein Data Bank code 1B39 )] and two active kinase co... formations [ADP-bound Aurora-A (magenta, Protein Data Bank code 1OL5 ) and ATP-bound Cdk2 (blue, Protein Data Bank code 1QMZ )].
The interwinding nature of protein-protein interfaces and its implication for protein complex formation.
(2009) Bioinformatics 25
PubMed: 19789269 | PubMedCentral: PMC2778332 | DOI: 10.1093/bioinformatics/btp563
The maximum SF values of the two fragments, namely Ile35-Val44 and Leu148-Glu162 (PDB ID: 1QMZ chain A), are 1.14 and 0.97, respectively, which are high, although below the cutoff of 1.25 used here.
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
In addition, the proline in the Thr-Pro motif was restrained to adopt a similar binding mode to that in Ser-Pro motif of HHASPRK bound to the cyclin-dependent kinase (CDK2) (PDB ID: 1QMZ).
Publication Year: 2011
Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1.
(2011) BMC Biol 9
PubMed: 21729334 | PubMedCentral: PMC3158555 | DOI: 10.1186/1741-7007-9-48
Coordinates are from PDB ID: 1hcl (apo-CDK2), 1b39 (ATP-bound CDK2), 1qmz (ATP-bound CDK2 with cyclin) and 1gy3 (ADP-bound CDK2 with cyclin).
Fluorescent peptide biosensor for probing the relative abundance of cyclin-dependent kinases in living cells.
PubMed: 22028905 | PubMedCentral: PMC3196589 | DOI: 10.1371/journal.pone.0026555
A. Sequence and schematic representation of CDKSENS together with the crystal structures of CDK2/cyclin A/HHASPRK peptide substrate (PDB 1QMZ) and CDK2/cyclin A/p107 RRLFGE peptide (PDB 1H28).
Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa.
(2011) BMC Evol Biol 11
PubMed: 22047078 | PubMedCentral: PMC3239843 | DOI: 10.1186/1471-2148-11-321
In a solved structure of human Cdk2 [PDB: 1QMZ ], the residue V164, equivalent to C258 in Pfcrk-5, is located spatially between the bound substrate and the APE motif.
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 ].
The structure figures were generated in PyMOL based on the crystal structure of cyclin-dependent kinase (pdb: 1QMZ).
Publication Year: 2012
Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase.
(2012) J Am Chem Soc 134
PubMed: 22891849 | PubMedCentral: PMC3446636 | DOI: 10.1021/ja304419t
The backbone rmsd from ADP·2Mg structure to 1JST (a complex with ATPγS·Mn 2+ ) = 1.24 Å, 1QMZ (AMPPNP·Mg 2+ /peptide) = 0.65 Å, 3QHR (ADP·2Mg/Mg... 3 – /peptide TS) = 0.57 Å.
(C) Two Mg 2+ ions are identified in the ADP·2Mg structure (maroon) but not ATPγS-bound pCDK2 (gray, 1JST) 3 or AMPPNP-bound pCDK2 (black, 1QMZ).
The CDK9 tail determines the reaction pathway of positive transcription elongation factor b.
(2012) Structure 20
PubMed: 22959624 | PubMedCentral: PMC3469819 | DOI: 10.1016/j.str.2012.08.011
Modeling of a CDK9/Cyclin T/Substrate Complex The polypeptide backbone of the CDK9 FL /cyclin T 259 /DRB and CDK2/cyclin A/peptide (1QMZ) complexes were superimposed on the C-terminal kinase domain (r... sidues 111–315 and 88–286, respectively) and the substrate peptide was copied into the CDK9/cyclin T 259 structure.
Comparative structural and functional studies of 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile CDK9 inhibitors suggest the basis for isotype selectivity.
(2013) J Med Chem 56
PubMed: 23252711 | PubMedCentral: PMC3579457 | DOI: 10.1021/jm301495v
(D) Detail of the conformational change induced by the binding of 3 and 12t (cylinder representation) on CDK2/cyclin A (blue ribbon representation), relative to CDK2/cyclin A in the absence of inhibit... r (PDB code 1QMZ , yellow ribbon representation).
(B) The protein conformations in representative novel CDK2/cyclin A/inhibitor structures (blue ribbon representations) are compared with that of CDK2/cyclin A in the absence of inhibitor (PDB code 1QMZ , yellow ribbon representation).
Publication Year: 2013
A structure-guided approach for protein pocket modeling and affinity prediction.
(2013) J Comput Aided Mol Des 27
PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9
Figure 2 shows the cognate ligands of these structures (molecules 4–9 , respectively corresponding to 1QMZ, 1KE6, 1KE8, 1JVP, and 1H07).
PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP, 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.
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
An inhibitor's-eye view of the ATP-binding site of CDKs in different regulatory states.
(2014) ACS Chem Biol 9
PubMed: 24669831 | PubMedCentral: PMC4068217 | DOI: 10.1021/cb500135f
The CDK2 ATP-binding site residues from a pCDK2/A structure (PDB code: 1QMZ) are colored according to the degree of sequence conservation between the 4 CDK sequences, calculated as described in the Su... plementary Methods , from blue (highly conserved) to red (highly variable).
Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy.
(2014) Oncotarget 5
PubMed: 25003367 | PubMedCentral: PMC4116514 | DOI: null
(B) A substrate peptide binding pocket of CDK2 (PDB ID: 1QMZ).
Exploiting holistic approaches to model specificity in protein phosphorylation.
(2014) Front Genet 5
PubMed: 25324856 | PubMedCentral: PMC4179730 | DOI: 10.3389/fgene.2014.00315
The structures from left to right show IR in complex with a peptide (pdb 1IR3), CDK2 in complex with a substrate peptide and cyclin A (pdb 1QMZ), which contributes to peptide specificity with a negati... e charged surface shown in the upper right of the figure, and PKA in complex with a peptide inhibitor (pdb 3FJQ).
Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II.
(2014) Molecules 19
PubMed: 24473209 | PubMedCentral: PMC4350670 | DOI: 10.3390/molecules19021481
( A ) Phosphorylated CDK2 (green) at its activation loop on T160 shown with its substrate HHASPRK (yellow) where P+1 position is occupied by proline (PDB ID: 1QMZ) [ 87 ].
PubMed ID is not available.
Published in 2015
A) Structural alignment of MAPK β4-β5 loop with representative canonical CMGC kinase, where orange denotes Casen Kinase II (CK2) (PDBID: 1JWH), green denotes cyclin dependent kinase (C... K) (PDBID: 1QMZ), and blue denotes MAPK with insert colored in cyan with rectangle representation (PDBID: 4LOO).
Publication Year: 2015
( A ) Structural representation of CDK2; ( B ) Structural representation of CDK2/Cyclin A complex (PDB: 1QMZ); ( C ) Structural representation of phospho Thr160-CDK2/Cyclin A; ( D ) Structural represe... tation of phospho Thr160-CDK2/Cyclin A bound to a peptide substrate.
( A ) Structure and inhibitors of CDK2/Cyclin A PDB: 1QMZ; ( B ) Structure and inhibitors of CDK4/Cyclin D PDB 3G33 [CycD3]; ( C ) Structure and inhibitors of CDK5/p25.
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