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- PDB-1ap7: P19-INK4D FROM MOUSE, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ap7
TitleP19-INK4D FROM MOUSE, NMR, 20 STRUCTURES
ComponentsP19-INK4D
KeywordsCELL CYCLE INHIBITOR / CYCLIN DEPENDENT KINASE INHIBITOR / INK / CDKI / ANKYRIN REPEAT
Function / homology
Function and homology information


cyclin D2-CDK4 complex / autophagic cell death / negative regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to vitamin D / DNA synthesis involved in DNA repair / regulation of G1/S transition of mitotic cell cycle / response to UV ...cyclin D2-CDK4 complex / autophagic cell death / negative regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to vitamin D / DNA synthesis involved in DNA repair / regulation of G1/S transition of mitotic cell cycle / response to UV / response to retinoic acid / sensory perception of sound / negative regulation of cell growth / cell cycle / negative regulation of cell population proliferation / protein kinase binding / nucleoplasm / cytosol
Similarity search - Function
Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Cyclin-dependent kinase 4 inhibitor D
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / XPLOR SA WITH AMBIGUOUS RESTRAINTS
AuthorsArcher, S.J. / Luh, F.Y. / Domaille, P.J. / Smith, B.O. / Laue, E.D.
CitationJournal: Nature / Year: 1997
Title: Structure of the cyclin-dependent kinase inhibitor p19Ink4d.
Authors: Luh, F.Y. / Archer, S.J. / Domaille, P.J. / Smith, B.O. / Owen, D. / Brotherton, D.H. / Raine, A.R. / Xu, X. / Brizuela, L. / Brenner, S.L. / Laue, E.D.
History
DepositionJul 25, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P19-INK4D


Theoretical massNumber of molelcules
Total (without water)17,9771
Polymers17,9771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30LOWEST ENERGY STRUCTURES WITH NO VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein P19-INK4D / CYCLIN DEPENDENT KINASE 4 INHIBITOR D


Mass: 17976.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q60773

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D N13 NOESY
1214D N15 NOESY
1313D C13 NOESY
1414D C13 NOESY
1513D HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED P19INK4D. ADDITIONAL RESTRAINTS WERE DETERMINED FROM NMR ON 2H, 15N-LABELED P19INK4D AND SELECTIVELY LABELED P19INK4D.

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Sample preparation

DetailsContents: 20MM SODIUM PHOSPHATE
Sample conditionsIonic strength: 100mM NACL, 1mM EDTA, 5mM DTT / pH: 7.5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Azarastructure solution
ANSIGstructure solution
XPLORstructure solution
PIPPstructure solution
NMRPipestructure solution
RefinementMethod: XPLOR SA WITH AMBIGUOUS RESTRAINTS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY STRUCTURES WITH NO VIOLATIONS
Conformers calculated total number: 30 / Conformers submitted total number: 20

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