2C5V Cell Cycle date Nov 02, 2005
title Differential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug Design
authors G.Kontopidis, C.Mcinnes, S.R.Pandalaneni, I.Mcnae, D.Gibson, M.Mezna, M.Thomas, G.Wood, S.Wang, M.D.Walkinshaw, P.M.Fischer
compound source
Molecule: Cell Division Protein Kinase 2
Chain: A, C
Synonym: Cyclin-Dependent Kinase 2, P33 Protein Kinase
Ec: 2.7.1.37
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus

Molecule: Cyclin A2
Chain: B, D
Synonym: Cyclin A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Aba-Arg-Ser-Leu-Ile-Pff-Nh2
Chain: F, H

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.171 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.501 114.549 156.994 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.9 Å
ligand ABA, CK4, NH2, PFF BindingDB enzyme Transferase E.C.2.7.1.37 BRENDA
note 2C5V supersedes 1OKU
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceDifferential binding of inhibitors to active and inactive CDK2 provides insights for drug design., Kontopidis G, McInnes C, Pandalaneni SR, McNae I, Gibson D, Mezna M, Thomas M, Wood G, Wang S, Walkinshaw MD, Fischer PM, Chem Biol. 2006 Feb;13(2):201-11. PMID:16492568
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (200 Kb) [Save to disk]
  • Biological Unit Coordinates (2c5v.pdb1.gz) 96 Kb
  • Biological Unit Coordinates (2c5v.pdb2.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 2C5V
  • CSU: Contacts of Structural Units for 2C5V
  • Likely Quarternary Molecular Structure file(s) for 2C5V
  • Structure Factors (411 Kb)
  • Retrieve 2C5V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2C5V from S2C, [Save to disk]
  • Re-refined 2c5v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2C5V in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2C5V
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2C5V, from MSDmotif at EBI
  • Fold representative 2c5v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2c5v_B] [2c5v] [2c5v_H] [2c5v_C] [2c5v_A] [2c5v_F] [2c5v_D]
  • SWISS-PROT database: [P20248] [P24941]
  • Domain organization of [CCNA2_HUMAN] [CDK2_HUMAN] by SWISSPFAM
  • Domains found in 2C5V: [CYCLIN] [Cyclin_C] [S_TKc ] by SMART
  • Other resources with information on 2C5V
  • Community annotation for 2C5V at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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