+Open data
-Basic information
Entry | Database: PDB / ID: 1qmz | ||||||
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Title | PHOSPHORYLATED CDK2-CYCLYIN A-SUBSTRATE PEPTIDE COMPLEX | ||||||
Components |
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Keywords | CELL CYCLE / COMPLEX (PROTEIN KINASE-CYCLIN) / CYCLIN / CDK / PHOSPHORYLATION / SUBSTRATE COMPLEX | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Brown, N.R. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N. | ||||||
Citation | Journal: Nat.Cell Biol. / Year: 1999 Title: The Structural Basis for Specificity of Substrate and Recruitment Peptides for Cyclin-Dependent Kinases Authors: Brown, N.R. / Noble, M.E. / Endicott, J.A. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qmz.cif.gz | 256 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qmz.ent.gz | 203 KB | Display | PDB format |
PDBx/mmJSON format | 1qmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qmz_validation.pdf.gz | 561.7 KB | Display | wwPDB validaton report |
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Full document | 1qmz_full_validation.pdf.gz | 621.7 KB | Display | |
Data in XML | 1qmz_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 1qmz_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/1qmz ftp://data.pdbj.org/pub/pdb/validation_reports/qm/1qmz | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | BIOLOGICAL_UNIT: HETERODIMER OF DIMERS |
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 34143.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PHOSPHORYLATED / Source: (gene. exp.) HOMO SAPIENS (human) Description: CYCLIN A-BOUND FORM PHOSPHORYLATED SOURCE COEXPRESSION WITH CAK1P Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | Mass: 29753.410 Da / Num. of mol.: 2 / Fragment: RESIDUES 174-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P20248 |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 835.953 Da / Num. of mol.: 2 / Fragment: 1-7 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) |
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-Non-polymers , 3 types, 771 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THREONINE 160 IN CHAINS A AND C HAS BEEN PHOSPHORYL |
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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: 3.54 Å3/Da / Density % sol: 65.21 % | ||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 22, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 51615 / % possible obs: 95.4 % / Observed criterion σ(I): 2.6 / Redundancy: 2.6 % / Rmerge(I) obs: 0.12 / Rsym value: 0.101 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 95.4 |
Reflection shell | *PLUS % possible obs: 95.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CDK2-CYCLIN A-RECRUITMENT PEPTIDE STRUCTURE SUBMITTED ALONG WITH THIS STRUCTURE Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2.6
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Displacement parameters | Biso mean: 34.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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