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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


: / cellular response to cell-matrix adhesion / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of phosphorylation / intestinal epithelial cell maturation / tissue regeneration / PCNA-p21 complex ...: / cellular response to cell-matrix adhesion / negative regulation of cyclin-dependent protein kinase activity / negative regulation of cardiac muscle tissue regeneration / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of phosphorylation / intestinal epithelial cell maturation / tissue regeneration / PCNA-p21 complex / regulation of cell cycle G1/S phase transition / import into nucleus / Transcriptional regulation by RUNX2 / negative regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to arsenic-containing substance / oncogene-induced cell senescence / Transcriptional activation of cell cycle inhibitor p21 / positive regulation of programmed cell death / AKT phosphorylates targets in the cytosol / RUNX3 regulates CDKN1A transcription / regulation of cyclin-dependent protein serine/threonine kinase activity / stress-induced premature senescence / response to corticosterone / molecular function inhibitor activity / cellular response to UV-B / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / p53-Dependent G1 DNA Damage Response / protein kinase inhibitor activity / 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) / regulation of G1/S transition of mitotic cell cycle / keratinocyte proliferation / replicative senescence / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / positive regulation of protein kinase activity / response to hyperoxia / animal organ regeneration / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / keratinocyte differentiation / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / protein serine/threonine kinase binding / positive regulation of B cell proliferation / Signaling by FLT3 fusion proteins / intrinsic apoptotic signaling pathway / cellular response to amino acid starvation / protein sequestering activity / cyclin binding / molecular function activator activity / positive regulation of DNA replication / cellular response to ionizing radiation / wound healing / cellular response to gamma radiation / negative regulation of cell growth / DNA Damage/Telomere Stress Induced Senescence / SCF(Skp2)-mediated degradation of p27/p21 / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / response to toxic substance / positive regulation of fibroblast proliferation / protein import into nucleus / positive regulation of reactive oxygen species metabolic process / Cyclin D associated events in G1 / cellular senescence / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / Neddylation / cellular response to heat / heart development / Senescence-Associated Secretory Phenotype (SASP) / fibroblast proliferation / Interleukin-4 and Interleukin-13 signaling / in utero embryonic development / Ras protein signal transduction / regulation of cell cycle / nuclear body / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / zinc ion binding / 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
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: p21


Theoretical massNumber of molelcules
Total (without water)1,8011
Polymers1,8011
Non-polymers00
Water00
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
Has protein modificationY

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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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