Citations in PubMed

Primary Citation PubMed: 8684460 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 10

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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An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data.

(2007) BMC Pharmacol 7

PubMed: 17705877 | PubMedCentral: PMC2045083 | DOI: 10.1186/1471-2210-7-10

(c) Location of a pocket laid across CDK2 and CDKN1B on CDK2/CDKN1B/cyclin A complex [PDB: 1JSU ].

Instead of 1V1K_A, we further investigated a tertiary structure of protein complex [PDB: 1JSU ] composed of CDK2, cyclin A, and CDKN1B that is a homolog of CDKN1A (sequence identity < 45%).

Publication Year: 2007


Prediction of protein binding regions in disordered proteins.

(2009) PLoS Comput Biol 5

PubMed: 19412530 | PubMedCentral: PMC2671142 | DOI: 10.1371/journal.pcbi.1000376

Bottom: Crystal structure of human p27 (red and yellow) complexed with CDK2 (magenta) and Cyclin A (blue) (PDB ID: 1jsu [62] ).

Its kinase inhibitory domain binds both subunits of the CDK2-cyclin A complex in an extended conformation (PDB ID: 1jsu [62] ).

Publication Year: 2009


Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective.

(2010) BMC Bioinformatics 11

PubMed: 20462403 | PubMedCentral: PMC2882391 | DOI: 10.1186/1471-2105-11-244

PDB entry First Chains Second Chains 1AD3 -A:B VAL396-THR398-LEU399 VAL86-LEU97 1B7B -A:C THR109-VAL110-LEU111 VAL110-LEU111 1B8J -A:B LEU33-THR81-VAL430 LEU80-VAL430 1LDJ -A:B VAL539-LEU540-THR580 VA... 30-LEU32 1QOE -A:B LEU250-VAL261-THR262 LEU250-VAL261 Table 6 Interactions involving the DWE biclique = ⟨{ALA, LEU, VAL},{LEU, TYR}⟩ occurring in both obligate and non-obligate interactions PDB entry First Chains Second Chains Interaction Type 1AT3 -A:B LEU214-ALA217-VAL218 TYR124-LEU213 Obligate 1GO3 -E:F VAL12-ALA17-LEU41 TYR2-LEU75 Obligate 1DOA -A:B VAL36-ALA59-LEU67 LEU48-TYR51 Non-obligate 1EVT -A:C LEU165-ALA167-VAL168 TYR15-LEU135 Non-obligate 1JSU -A:C VAL18-ALA31-LEU83 LEU84-TYR88 Non-obligate Table 7 Interactions involving the uniquebiclique = ⟨{GLN, GLY, SER, SER, TYP},{CYS, LYS}⟩ of non-obligate interactions.

Publication Year: 2010


Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21.

(2011) Nat Chem Biol 7

PubMed: 21358637 | PubMedCentral: PMC3124363 | DOI: 10.1038/nchembio.536

However, we analyzed crystallographic B-factors for amide N atoms reported in the coordinate file (1JSU 17 ) ( Fig. 2b ).

In ( a ), the structure of p21-KID bound to Cdk2/cyclin A was modeled using that of p27-KID bound to Cdk2/cyclin A (1JSU 17 ).

1 Anfinsen CB Principles that govern the folding of protein chains Science 181 223 30 1973 4124164 2 Martin AC Protein folds and functions Structure 6 875 84 1998 9687369 3 Dyson HJ Wright PE Intrinsically unstructured proteins and their functions Nat Rev Mol Cell Biol 6 197 208 2005 15738986 4 Dunker AK Obradovic Z Romero P Garner EC Brown CJ Intrinsic protein disorder in complete genomes Genome Inform Ser Workshop Genome Inform 11 161 71 2000 5 Dyson HJ Wright PE Coupling of folding and binding for unstructured proteins Curr Opin Struct Biol 12 54 60 2002 11839490 6 Lacy ER p27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein folding Nat Struct Mol Biol 11 358 364 2004 15024385 7 Kriwacki RW Hengst L Tennant L Reed SI Wright PE Structural studies of p21(waf1/cip1/sdi1) in the free and Cdk2-bound state: Conformational disorder mediates binding diversity Proc Natl Acad Sci USA 93 11504 11509 1996 8876165 8 Tompa P Szasz C Buday L Structural disorder throws new light on moonlighting Trends Biochem Sci 30 484 9 2005 16054818 9 Sherr CJ Roberts JM Inhibitors of mammalian G1 cyclin-dependent kinases Genes Dev 15 1149 63 1995 7758941 10 Morgan DO Principles of CDK regulation Nature 374 131 134 1995 7877684 11 Weinbeg RA The Biology of Cancer Garland Science London 2006 12 Xiong Y p21 is a universal inhibitor of cyclin kinases Nature 366 701 704 1993 8259214 13 Harper JW Inhibition of cyclin-dependent kinases by p21 Mol Biol Cell 6 387 400 1995 7626805 14 Zhang H Xiong Y Beach D Proliferating cell nuclear antigen and p21 are components of multiple cell cycle kinase complexes Molecular Biology of the Cell 4 897 906 1993 7903056 15 Cheng M The p21(Cip1) and p27(Kip1) CDK ‘inhibitors’ are essential activators of cyclin D-dependent kinases in murine fibroblasts EMBO J 18 1571 83 1999 10075928 16 Galea CA Wang Y Sivakolundu SG Kriwacki RW Regulation of cell division by intrinsically unstructured proteins: intrinsic flexibility, modularity, and signaling conduits Biochemistry 47 7598 609 2008 18627125 17 Russo AA Jeffrey PD Patten AK Massague J Pavletich NP Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex Nature 382 325 331 1996 8684460 18 Wang Y Filippov I Richter C Luo R Kriwacki RW Solution NMR studies of an intrinsically unstructured protein within a dilute, 75 kDa eukaryotic protein assembly; probing the practical limits for efficiently assigning polypeptide backbone resonances Chembiochem 6 2242 6 2005 16270364 19 Schwarzinger S Sequence-dependent correction of random coil NMR chemical shifts J Am Chem Soc 123 2970 8 2001 11457007 20 Wishart DS Sykes BD Chemical shifts as a tool for structure determination Meth Enzymol 239 363 392 1994 7830591 21 Kriwacki RW Wu J Siuzdak G Wright PE Probing Protein/Protein Interactions with Mass Spectrometry and Isotopic Labeling: Analysis of the p21/Cdk2 Complex J Amer Chem Soc 118 5320 5321 1996 22 Harper JW Inhibition of cyclin-dependent kinases by p21 Mol Biol Cell 6 387 400 1995 7626805 23 Arnold K Bordoli L Kopp J Schwede T The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling Bioinformatics 22 195 201 2006 16301204 24 Creighton TE Protein Structure, A Practical Approach IRL Press New York 1989 25 Schulman BA Lindstrom DL Harlow E Substrate recruitment to cyclin-dependent kinase 2 by a multipurpose docking site on cyclin A Proc Natl Acad Sci U S A 95 10453 8 1998 9724724 26 Lacy ER Molecular Basis for the Specificity of p27 Toward Cyclin-dependent Kinases that Regulate Cell Division J Mol Biol 349 764 73 Epub 2005 Apr 26 2005 15890360 27 Bowman P Galea CA Lacy E Kriwacki RW Thermodynamic characterization of interactions between p27(Kip1) and activated and non-activated Cdk2: intrinsically unstructured proteins as thermodynamic tethers Biochim Biophys Acta 1764 182 9 Epub 2006 Jan 11 2006 16458085 28 Grimmler M Cdk-Inhibitory Activity and Stability of p27(Kip1) Are Directly Regulated by Oncogenic Tyrosine Kinases Cell 128 269 80 2007 17254966 29 Zindy F Myc signaling via the ARF tumor suppressor regulates p53-dependent apoptosis and immortalization Genes Dev 12 2424 2433 1998 9694806 30 Sherr CJ Roberts JM Cdk inhibitors: positive and negative regulators of G1-phase progression Genes Dev 13 1501 1512 1999 10385618 31 Hirai H Roussel MF Kato JY Ashmun RA Sherr CJ Novel INK4 proteins, p19 and p18, are specific inhibitors of the cyclin D-dependent kinases CDK4 and CDK6 Mol Cell Biol 15 2672 81 1995 7739547 32 Harper JW Adami GR Wei N Keyomarsi K Elledge SJ The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases Cell 75 805 816 1993 8242751 33 Bunz F Requirement for p53 and p21 to sustain G2 arrest after DNA damage Science 282 1497 501 1998 9822382 34 Galea CA Role of intrinsic flexibility in signal transduction mediated by the cell cycle regulator, p27 Kip1 J Mol Biol 376 827 38 2008 18177895 35 Sherr CJ Roberts JM Living with or without cyclins and cyclin-dependent kinases Genes Dev 18 2699 711 2004 15545627 36 Brown NR Cyclin B and cyclin A confer different substrate recognition properties on CDK2 Cell Cycle 6 1350 9 2007 17495531 37 Honda R The structure of cyclin E1/CDK2: implications for CDK2 activation and CDK2-independent roles EMBO J 24 452 63 Epub 2005 Jan 20 2005 15660127 38 Day PJ Crystal structure of human CDK4 in complex with a D-type cyclin Proc Natl Acad Sci U S A 106 4166 70 2009 19237565 39 Takaki T The structure of CDK4/cyclin D3 has implications for models of CDK activation Proc Natl Acad Sci U S A 106 4171 6 2009 19237555 40 Mittag T Forman-Kay JD Atomic-level characterization of disordered protein ensembles Curr Opin Struct Biol 17 3 14 2007 17250999 41 Sivakolundu SG Bashford D Kriwacki RW Disordered p27 (Kip1) Exhibits Intrinsic Structure Resembling the Cdk2/Cyclin A-bound Conformation J Mol Biol 353 1118 1128 Epub 2005 Sep 20 2005 16214166 42 Neidhardt FC Bloch PL Smith DF Culture medium for enterobacteria J Bact 119 736 747 1974 4604283 43 Creighton TE Proteins: Structures and Molecular Properties W. H. Freeman & Co New York, NY 1993 44 Zhou P Lugovskoy AA Wagner G A solubility-enhancement tag (SET) for NMR studies of poorly behaving proteins J Biomol NMR 20 11 14 2001 11430750 45 Schwarzinger S Sequence-dependent correction of random coil NMR chemical shifts J Amer Chem Soc 123 2970 2978 2001 11457007 46 Zhu G Xia Y Nicholson LK Sze KH Protein dynamics measurements by TROSY-based NMR experiments J Magn Reson 143 423 6 2000 10729271 47 Delaglio F NMR Pipe: A multidimensional spectral processing system based on UNIX pipes J Biomol NMR 6 277 293 1995 8520220 48 Cavanagh J Fairbrother WJ Palmer AG III Rance M Skelton NJ Protein NMR spectroscopy: Principle and Practice Academic Press New York 2007 49 Bowman P Galea CA Lacy E Kriwacki RW Thermodynamic characterization of interactions between p27 (Kip1) and activated and non-activated Cdk2: intrinsically unstructured proteins as thermodynamic tethers Biochim Biophys Acta 1764 182 9 2006 16458085 Figure 1 p21 and p27 adopt similar secondary structure when bound to Cdk2/cyclin A. ( a ) Structure of p27-KID bound to Cdk2/cyclin A (PDB 1JSU 17 ) showing sub-domains D1 (blue), LH (red) and D2 (green) of p27-KID.

( b ) B-factor values for backbone amide N atoms for p27-KID within the ternary complex with Cdk2/cyclin A (PDB 1JSU).

Publication Year: 2011


IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.

(2012) Nucleic Acids Res 40

PubMed: 22067451 | PubMedCentral: PMC3245138 | DOI: 10.1093/nar/gkr884

Some relatively long IDRs, such as p27Kip1 (PDB:1jsu) and Tcf3 (PDB:1g3j), can transform into ordered states ( 22 ).

Publication Year: 2012


Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces.

(2012) BMC Bioinformatics 13

PubMed: 22452998 | PubMedCentral: PMC3373366 | DOI: 10.1186/1471-2105-13-51

All of them are hydrolase-inhibitor interfaces, except one cyclin A-cyclin-dependent kinase 2 interaction [PDB: 1JSU ] and one Cell division protein kinase 2 [PDB: 2CO5 ].

Publication Year: 2012


Probing the role of nascent helicity in p27 function as a cell cycle regulator.

(2012) PLoS One 7

PubMed: 23071750 | PubMedCentral: PMC3470550 | DOI: 10.1371/journal.pone.0047177

The input used for the program was the pdb file of the p27-KID/Cdk2/cyclin A complex (1JSU).

The PDB file, 1JSU, was used as an input and all the atoms within a 6 Å radius of every atom of each candidate residue were analyzed.

In this complex (PDB accession code 1JSU), the D1 sub-domain of p27 adopts an extended conformation upon binding the cyclin A subunit of the complex, sub-domain LH folds into an amphipathic α-helix, and sub-domain D2 folds into amphipathic β-hairpin, a β-strand, and a 3 10 helix on binding Cdk2.

Publication Year: 2012


Protein flexibility, not disorder, is intrinsic to molecular recognition.

(2013) F1000 Biol Rep 5

PubMed: 23361309 | PubMedCentral: PMC3542771 | DOI: 10.3410/B5-2

The p27 Kip1 -Cdk2-cyclin A ternary complex In the crystal structure [ 55 ] (Protein Data Bank entry 1JSU), the kinase inhibitory domain of p27 Kip1 (KID, in green) is observed to be partly helical an... interact with both the kinase and the cyclin.

Publication Year: 2013


On the importance of polar interactions for complexes containing intrinsically disordered proteins.

(2013) PLoS Comput Biol 9

PubMed: 23990768 | PubMedCentral: PMC3749945 | DOI: 10.1371/journal.pcbi.1003192

(b) Ribbon structure of the ID segment of p27 (red) that “wraps” around its complex partners cyclin A (grey) and Cdk2 (gold) (p27; PDB: 1JSU chain C, Rg = 21 Å,... N = 69).

Publication Year: 2013


Molecular Docking of Known Carcinogen 4- (Methyl-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) with Cyclin Dependent Kinases towards Its Potential Role in Cell Cycle Perturbation.

(2014) Bioinformation 10

PubMed: 25258489 | PubMedCentral: PMC4166773 | DOI: 10.6026/97320630010526

The structures of the cell cycle regulatory proteins CDKs (CDK8:3RGF, CDK2:3DDP, CDK7:1UA2, CDK6:1BLX, CDK9:3BLH & CDK4:3G33) obtained from PDB and other complementary partner protein cyclin (... yclin A: 1JSU, cyclin H: 1KXU, cyclin D3: 3G33, cyclin D: 2W9F, cyclin C: 1ZP2 and cyclin T: 3BLR) were retrieved from MODBASE server.

Publication Year: 2014