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- PDB-1ol1: Cyclin A binding groove inhibitor H-Cit-Cit-Leu-Ile-(p-F-Phe)-NH2 -

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Basic information

Entry
Database: PDB / ID: 1ol1
TitleCyclin A binding groove inhibitor H-Cit-Cit-Leu-Ile-(p-F-Phe)-NH2
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CIR-CIR-LEU-ILE-PFF-NH2
  • CYCLIN A2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / CELL CYCLE / KINASE-CYCLIN COMPLEX / CYCLIN A / INHIBITOR / LIGAND EXCHANGE / DRUG DESIGN / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL DIVISION / MITOSIS / PHOSPHORYLATION / PEPTIDOMIMETICS
Function / homology
Function and homology information


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 anaphase-promoting complex-dependent catabolic process / regulation of DNA replication / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Cajal body / animal organ regeneration / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Activation of ATR in response to replication stress / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / male germ cell nucleus / response to organic substance / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / 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 / Cyclin D associated events in G1 / positive regulation of fibroblast proliferation / G2/M transition of mitotic cell cycle / cellular senescence / 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 / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / cell division / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKontopidis, 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.
CitationJournal: Structure / Year: 2003
Title: Insights Into Cyclin Groove Recognition. Complex Crystal Structures and Inhibitor Design Through Ligand Exchange
Authors: 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.
History
DepositionAug 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 15, 2017Group: Database references / Source and taxonomy
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
F: CIR-CIR-LEU-ILE-PFF-NH2
H: CIR-CIR-LEU-ILE-PFF-NH2


Theoretical massNumber of molelcules
Total (without water)129,1326
Polymers129,1326
Non-polymers00
Water1,31573
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
F: CIR-CIR-LEU-ILE-PFF-NH2


Theoretical massNumber of molelcules
Total (without water)64,5663
Polymers64,5663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-10 kcal/mol
Surface area23570 Å2
MethodPISA
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
H: CIR-CIR-LEU-ILE-PFF-NH2


Theoretical massNumber of molelcules
Total (without water)64,5663
Polymers64,5663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-5 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.498, 113.471, 154.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 2 / / CYCLIN-DEPENDENT KINASE 2 / P33 PROTEIN KINASE


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
#2: Protein CYCLIN A2 / / CYCLIN A


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 CIR-CIR-LEU-ILE-PFF-NH2


Mass: 721.845 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CYCLIN GROOVE-BOUND PEPTIDE CIT-CIT-LEU-ILE-PFF-NH2
Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: INVOLVED IN THE CONTROL OF THE CELL CYCLE. ACTIVITY OF CDK2 IS MAXIMAL DURING S PHASE AND G2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.8 / Details: 22% PEG 3350, 0.1M NA3-CIT, PH 7.80
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17-8 mg/mlprotein1drop
240 mMHEPES1droppH7.0
3200 mM1dropNaCl
45 mMdithiothreitol1drop
518 %PEG33501reservoir
6100 mMtrisodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. obs: 29357 / % possible obs: 98.9 % / Redundancy: 22.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 2.8
Reflection shellResolution: 2.9→3.06 Å / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 1.5 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. measured all: 648091 / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FIN

1fin


Resolution: 2.9→12 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.863 / SU B: 20.707 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1198 4.1 %RANDOM
Rwork0.206 ---
obs0.209 27895 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BULK SOLVENT
Displacement parametersBiso mean: 52.14 Å2
Baniso -1Baniso -2Baniso -3
1--3.91 Å20 Å20 Å2
2--1.73 Å20 Å2
3---2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9025 0 0 73 9098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229249
X-RAY DIFFRACTIONr_bond_other_d0.0020.028494
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9812555
X-RAY DIFFRACTIONr_angle_other_deg1.16319820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.41751104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.21424
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.029990
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021806
X-RAY DIFFRACTIONr_nbd_refined0.3310.33024
X-RAY DIFFRACTIONr_nbd_other0.3310.311318
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.10.55588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3050.5557
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.340
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3370.370
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5070.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3931.55553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.9129031
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.55233696
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it14.0984.53524
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.418 81
Rwork0.291 1950
Refinement
*PLUS
Rfactor Rfree: 0.291 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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