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- PDB-2wmb: Structural and thermodynamic consequences of cyclization of pepti... -
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Entry | Database: PDB / ID: 2wmb | ||||||
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Title | Structural and thermodynamic consequences of cyclization of peptide ligands for the recruitment site of cyclin A | ||||||
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![]() | CELL CYCLE / CELL DIVISION / ANTI-ONCOGENE / SERINE/THREONINE-PROTEIN KINASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / RECRUITMENT / TRANSCRIPTION / NUCLEUS / MITOSIS / ATP-BINDING / TRANSFERASE | ||||||
Function / homology | ![]() Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / response to glucagon ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / response to glucagon / cellular response to cocaine / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of DNA replication / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / cellular response to nitric oxide / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / : / cyclin binding / post-translational protein modification / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Robertson, G.F. / Endicott, J.A. / Noble, M.E.M. / McDonnell, J.M. | ||||||
![]() | ![]() Title: Structural and Thermodynamic Consequences of Cyclization of Peptide Ligands for the Recruitment Site of Cyclin A Authors: Robertson, G.F. / Endicott, J.A. / Noble, M.E.M. / Mcdonnell, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 230.3 KB | Display | ![]() |
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PDB format | ![]() | 185.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wmaC ![]() 1h28S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 34467.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #3: Protein/peptide | | Mass: 679.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.11 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: BUFFER: 10MM HEPES PH 7.0, 100MM NACL. 1.1 TO 1.25M AMMONIUM SULPHATE, 0.7 TO 0.85MM KCL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→22.04 Å / Num. obs: 46010 / % possible obs: 95 % / Observed criterion σ(I): 1.5 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.55→2.69 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7 / % possible all: 89.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H28 Resolution: 2.6→22.04 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.868 / SU B: 12.949 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.741 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→22.04 Å
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