1VYZ Transferase date May 07, 2004
title Structure Of Cdk2 Complexed With Pnu-181227
authors P.Pevarello, M.G.Brasca, R.Amici, P.Orsini, G.Traquandi, L.Corti, P.Sansonna, M.Villa, B.S.Pierce, M.Pulici, G.Giordano, K.Martina E.Lfritzen, R.A.Nugent, E.Casale, A.Cameron, M.Ciomei, F.Roletto A.Isacchi, G.Fogliatto, E.Pesenti, W.Pastori, W.Marsiglio, K.L.L P.M.Clare, F.Fiorentini, M.Varasi, A.Vulpetti, M.A.Warpehoski
compound source
Molecule: Cell Division Protein Kinase 2
Chain: A
Synonym: 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_taxid: 7108
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 21 21 21
R_factor 0.238 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.250 71.910 72.220 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.21 Å
ligand N5B BindingDB enzyme Transferase E.C.2.7.1.37 BRENDA
related structures by homologous chain: 1FVT, 1P5E
Gene
Ontology
ChainFunctionProcessComponent
A


Primary reference3-Aminopyrazole inhibitors of CDK2/cyclin A as antitumor agents. 1. Lead finding., Pevarello P, Brasca MG, Amici R, Orsini P, Traquandi G, Corti L, Piutti C, Sansonna P, Villa M, Pierce BS, Pulici M, Giordano P, Martina K, Fritzen EL, Nugent RA, Casale E, Cameron A, Ciomei M, Roletto F, Isacchi A, Fogliatto G, Pesenti E, Pastori W, Marsiglio A, Leach KL, Clare PM, Fiorentini F, Varasi M, Vulpetti A, Warpehoski MA, J Med Chem 2004 Jun 17;47(13):3367-80. PMID:15189033
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (1vyz.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 1VYZ
  • CSU: Contacts of Structural Units for 1VYZ
  • Likely Quarternary Molecular Structure file(s) for 1VYZ
  • Structure Factors (100 Kb)
  • Retrieve 1VYZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VYZ from S2C, [Save to disk]
  • Re-refined 1vyz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VYZ 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 1VYZ
  • 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 1VYZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vyza_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1vyz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vyz] [1vyz_A]
  • SWISS-PROT database: [P24941]
  • Domain organization of [CDK2_HUMAN] by SWISSPFAM
  • Domain found in 1VYZ: [S_TKc ] by SMART
  • Other resources with information on 1VYZ
  • Community annotation for 1VYZ 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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