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- PDB-1ol2: Cyclin A binding groove inhibitor H-Arg-Arg-Leu-Asn-(p-F-Phe)-NH2 -

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Basic information

Entry
Database: PDB / ID: 1ol2
TitleCyclin A binding groove inhibitor H-Arg-Arg-Leu-Asn-(p-F-Phe)-NH2
Components
  • ARG-ARG-LEU-ASN-PFF-NH2
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CELL CYCLE / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / CYCLIN A / LIGAND EXCHANGE / PEPTIDOMIMETICS / KINASE
Function / homology
Function and homology information


cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / mitotic cell cycle phase transition / male pronucleus / female pronucleus / cellular response to insulin-like growth factor stimulus / cellular response to leptin stimulus / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity ...cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / mitotic cell cycle phase transition / male pronucleus / female pronucleus / cellular response to insulin-like growth factor stimulus / cellular response to leptin stimulus / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cochlea development / cellular response to platelet-derived growth factor stimulus / regulation of DNA replication / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin A1-CDK2 complex / cyclin E1-CDK2 complex / cyclin E2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / cyclin A2-CDK2 complex / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / condensed chromosome / cyclin-dependent protein kinase holoenzyme complex / Cajal body / cellular response to nitric oxide / mitotic G1 DNA damage checkpoint / cyclin binding / regulation of gene silencing / potassium ion transport / meiotic cell cycle / cellular response to estradiol stimulus / chromosome, telomeric region / animal organ regeneration / G1/S transition of mitotic cell cycle / positive regulation of fibroblast proliferation / anaphase-promoting complex-dependent catabolic process / regulation of G2/M transition of mitotic cell cycle / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to hypoxia / Ras protein signal transduction / G2/M transition of mitotic cell cycle / transcription factor complex / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / protein deubiquitination / centrosome / cell division / DNA repair / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / viral process / positive regulation of cell population proliferation / protein kinase binding / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Protein kinase-like domain superfamily / Cyclin-A, N-terminal / Protein kinase domain / Cyclin, C-terminal domain / Cyclin, N-terminal / Serine/threonine-protein kinase, active site / Protein kinase, ATP binding site / Cyclin-like / Cyclin-like superfamily / Cyclin ...Protein kinase-like domain superfamily / Cyclin-A, N-terminal / Protein kinase domain / Cyclin, C-terminal domain / Cyclin, N-terminal / Serine/threonine-protein kinase, active site / Protein kinase, ATP binding site / Cyclin-like / Cyclin-like superfamily / Cyclin / Protein kinase domain / Cyclin, N-terminal domain / Cyclin, C-terminal domain / Cyclin-like / Cyclin A; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Cyclin-dependent kinase 2 / Cyclin-A2
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKontopidis, 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 5, 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 8, 2017Group: Other / Source and taxonomy

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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
E: ARG-ARG-LEU-ASN-PFF-NH2
F: ARG-ARG-LEU-ASN-PFF-NH2


Theoretical massNumber of molelcules
Total (without water)129,1346
Polymers129,1346
Non-polymers00
Water6,503361
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
E: ARG-ARG-LEU-ASN-PFF-NH2


Theoretical massNumber of molelcules
Total (without water)64,5673
Polymers64,5673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
F: ARG-ARG-LEU-ASN-PFF-NH2


Theoretical massNumber of molelcules
Total (without water)64,5673
Polymers64,5673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)73.540, 112.980, 153.089
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/peptide 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/peptide 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)
Description: CYCLIN GROOVE-BOUND PEPTIDE H-ARG-ARG-LEU-ASN-(P-F-PHE)-NH2
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P20248
#3: Protein/peptide ARG-ARG-LEU-ASN-PFF-NH2


Mass: 722.836 Da / Num. of mol.: 2
Details: CYCLIN GROOVE-BOUND PEPTIDE H-ARG-ARG-LEU-ASN-(P-F-PHE)-NH2
Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O / Water

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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

Crystal-ID: 1

IDConc.Common nameSol-IDDetailsChemical formula
17-8 mg/mlproteindrop
240 mMHEPESdroppH7.0
3200 mMdropNaCl
45 mMdithiothreitoldrop
518 %PEG3350reservoir
6100 mMtrisodium citratereservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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. measured all: 574133 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FIN
Resolution: 2.6→12 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.866 / SU B: 11.9 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 1.97 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1220 3.1 %RANDOM
Rwork0.191 ---
Obs0.194 38153 99.6 %-
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: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9025 0 0 361 9386
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0130.0229249
r_bond_other_d0.0030.028486
r_angle_refined_deg1.7591.9812555
r_angle_other_deg1.908319796
r_dihedral_angle_1_deg7.95251104
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_chiral_restr0.110.21422
r_gen_planes_refined0.0110.029998
r_gen_planes_other0.0120.021810
r_nbd_refined0.2350.32404
r_nbd_other0.2660.310209
r_nbtor_refined
r_nbtor_other0.0940.55367
r_xyhbond_nbd_refined0.2240.5456
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.2240.318
r_symmetry_vdw_other0.2520.366
r_symmetry_hbond_refined0.4170.511
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it3.8171.55553
r_mcbond_other
r_mcangle_it5.77329031
r_mcangle_other
r_scbond_it8.45233696
r_scbond_other
r_scangle_it12.1094.53524
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.6→2.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.429 76
Rwork0.316 2684
Refinement
*PLUS
Num. reflection obs: 36002 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.196

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