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- PDB-6civ: Lactam cyclised mimetic of a fragment of p21 -

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Basic information

Entry
Database: PDB / ID: 6civ
TitleLactam cyclised mimetic of a fragment of p21
Componentsp21
KeywordsBIOSYNTHETIC PROTEIN / PIP-box motif / p21 / constrained / peptidomimetic
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / PCNA-p21 complex / TFAP2 (AP-2) family regulates transcription of cell cycle factors / FOXO-mediated transcription of cell cycle genes / intestinal epithelial cell maturation / cellular response to extracellular stimulus / tissue regeneration / regulation of cell cycle G1/S phase transition ...cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / PCNA-p21 complex / TFAP2 (AP-2) family regulates transcription of cell cycle factors / FOXO-mediated transcription of cell cycle genes / intestinal epithelial cell maturation / cellular response to extracellular stimulus / tissue regeneration / regulation of cell cycle G1/S phase transition / Transcriptional regulation by RUNX2 / negative regulation of phosphorylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of DNA biosynthetic process / response to arsenic-containing substance / oncogene-induced cell senescence / positive regulation of programmed cell death / Transcriptional activation of cell cycle inhibitor p21 / RUNX3 regulates CDKN1A transcription / AKT phosphorylates targets in the cytosol / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / stress-induced premature senescence / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / response to corticosterone / cellular response to UV-B / molecular function inhibitor activity / protein kinase inhibitor activity / STAT5 activation downstream of FLT3 ITD mutants / p53-Dependent G1 DNA Damage Response / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / Constitutive Signaling by AKT1 E17K in Cancer / mitotic G2 DNA damage checkpoint signaling / negative regulation of vascular associated smooth muscle cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / keratinocyte proliferation / response to X-ray / replicative senescence / cyclin-dependent protein kinase holoenzyme complex / response to hyperoxia / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of protein kinase activity / positive regulation of DNA replication / animal organ regeneration / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin E associated events during G1/S transition / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of B cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / keratinocyte differentiation / response to organonitrogen compound / cellular response to amino acid starvation / regulation of G2/M transition of mitotic cell cycle / Signaling by FLT3 fusion proteins / cyclin binding / protein sequestering activity / intrinsic apoptotic signaling pathway / negative regulation of protein phosphorylation / negative regulation of protein binding / molecular function activator activity / cellular response to ionizing radiation / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / wound healing / negative regulation of cell growth / DNA Damage/Telomere Stress Induced Senescence / response to toxic substance / SCF(Skp2)-mediated degradation of p27/p21 / protein import into nucleus / Transcriptional regulation of granulopoiesis / The role of GTSE1 in G2/M progression after G2 checkpoint / positive regulation of reactive oxygen species metabolic process / Cyclin D associated events in G1 / KEAP1-NFE2L2 pathway / positive regulation of fibroblast proliferation / cellular senescence / cellular response to heat / Neddylation / heart development / fibroblast proliferation / Senescence-Associated Secretory Phenotype (SASP) / Interleukin-4 and Interleukin-13 signaling / Ras protein signal transduction / in utero embryonic development / nuclear body / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / negative regulation of gene expression / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm
Similarity search - Function
Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor
Similarity search - Domain/homology
Cyclin-dependent kinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWegener, K.L.
CitationJournal: Chemistry / Year: 2018
Title: Rational Design of a 310-Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp.
Authors: Wegener, K.L. / McGrath, A.E. / Dixon, N.E. / Oakley, A.J. / Scanlon, D.B. / Abell, A.D. / Bruning, J.B.
History
DepositionFeb 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: p21


Theoretical massNumber of molelcules
Total (without water)1,8011
Polymers1,8011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2120 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide p21


Mass: 1801.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P38936*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic12D COSY
141isotropic11D 1H

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Sample preparation

DetailsType: solution / Contents: 1.3 mM NA ACR2, 0.1 mM NA DSS, 90% H2O/10% D2O / Label: ACR2 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMACR2NA1
0.1 mMDSSNA1
Sample conditionsIonic strength: 0 M / Label: ACR2 / pH: 5.95 / PH err: 0.01 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz / Details: Cryoprobe

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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