+Open data
-Basic information
Entry | Database: PDB / ID: 1urc | |||||||||
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Title | Cyclin A binding groove inhibitor Ace-Arg-Lys-Leu-Phe-Gly | |||||||||
Components |
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Keywords | TRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX / INHIBITOR / LIGAND EXCHANGE / DRUG DESIGN / PEPTIDOMIMETICS | |||||||||
Function / homology | Function and homology information G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase ...G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Regulation of APC/C activators between G1/S and early anaphase / cellular response to leptin stimulus / male pronucleus / Telomere Extension By Telomerase / G0 and Early G1 / female pronucleus / response to glucagon / cellular response to cocaine / cellular response to nitric oxide / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cochlea development / cellular response to platelet-derived growth factor stimulus / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / regulation of DNA replication / animal organ regeneration / post-translational protein modification / cellular response to estradiol stimulus / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / Ub-specific processing proteases / protein domain specific binding / cell division / centrosome / DNA-templated transcription / positive regulation of DNA-templated transcription / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Kontopidis, G. / Andrews, M. / McInnes, C. / Cowan, A. / Powers, H. / Innes, L. / Plater, A. / Griffiths, G. / Paterson, D. / Zheleva, D. ...Kontopidis, G. / Andrews, M. / McInnes, C. / Cowan, A. / Powers, H. / Innes, L. / Plater, A. / Griffiths, G. / Paterson, D. / Zheleva, D. / Lane, D. / Green, S. / Walkinshaw, M. / Fischer, P. | |||||||||
Citation | Journal: Org. Biomol. Chem. / Year: 2004 Title: Design, synthesis, biological activity and structural analysis of cyclic peptide inhibitors targeting the substrate recruitment site of cyclin-dependent kinase complexes. Authors: Andrews, M.J. / McInnes, C. / Kontopidis, G. / Innes, L. / Cowan, A. / Plater, A. / Fischer, P.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1urc.cif.gz | 240.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1urc.ent.gz | 195.2 KB | Display | PDB format |
PDBx/mmJSON format | 1urc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1urc_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 1urc_full_validation.pdf.gz | 487.7 KB | Display | |
Data in XML | 1urc_validation.xml.gz | 29 KB | Display | |
Data in CIF | 1urc_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/1urc ftp://data.pdbj.org/pub/pdb/validation_reports/ur/1urc | HTTPS FTP |
-Related structure data
Related structure data | 1finS 1h0u S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P24941, EC: 2.7.1.37, cyclin-dependent kinase #2: Protein | Mass: 29867.512 Da / Num. of mol.: 2 / Fragment: RESIDUES 173 - 432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20248 #3: Protein/peptide | Mass: 647.810 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CYCLIN GROOVE-BOUND CYCLIC(2-5) PENTAPEPTIDE AC-ARG-LYS-LEU-PHE-GLY Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | Compound details | CYCLIN CONTROLS THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITIONS. KINASE ...CYCLIN CONTROLS THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: 22% PEG 3350, 0.1M NA3-CIT, pH 7.80 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Kontopidis, G., (2003) Structure, 11, 1537. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→17 Å / Num. obs: 39765 / % possible obs: 99.5 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.6→2.76 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1 / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 46681 / % possible obs: 98.9 % / Num. measured all: 113421 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.74 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FIN Resolution: 2.6→14 Å / SU B: 12.153 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 1.013 / ESU R Free: 0.327 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 42.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→14 Å
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Refinement | *PLUS Rfactor Rfree: 0.255 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |