1VYW Transferase date May 07, 2004
title Structure Of Cdk2cyclin A With Pnu-292137
authors P.Pevarello, M.G.Brasca, R.Amici, P.Orsini, G.Traquandi, L.Corti, P.Sansonna, M.Villa, B.S.Pierce, M.Pulici, P.Giordano, K.Martina E.L.Fritzen, R.A.Nugent, E.Casale, A.Cameron, M.Ciomei, F.Rolett A.Isacchi, G.Fogliatto, E.Pesenti, W.Pastori, A.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, C
Synonym: P33 Protein Kinase
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

Molecule: Cyclin A2
Chain: B, D
Fragment: C-Terminal Portion, Residues 174-432
Synonym: Cyclin A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_plasmid: Pgex6p
symmetry Space Group: P 62 2 2
R_factor 0.229 R_Free 0.258
length a length b length c angle alpha angle beta angle gamma
184.223 184.223 214.720 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand 292, SO4 BindingDB enzyme Transferase E.C. BRENDA
related structures by homologous chain: 1OIY, 1PKD, 1PXP
A, C

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] (198 Kb) [Save to disk]
  • Biological Unit Coordinates (1vyw.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (1vyw.pdb2.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 1VYW
  • CSU: Contacts of Structural Units for 1VYW
  • Likely Quarternary Molecular Structure file(s) for 1VYW
  • Structure Factors (2100 Kb)
  • Retrieve 1VYW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VYW from S2C, [Save to disk]
  • Re-refined 1vyw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VYW 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 1VYW
  • 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 1VYW, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vywa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vywb1, region B:175-309 [Jmol] [rasmolscript] [script source]
        - Domain d1vywb2, region B:310-432 [Jmol] [rasmolscript] [script source]
        - Domain d1vywc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1vywd1, region D:178-309 [Jmol] [rasmolscript] [script source]
        - Domain d1vywd2, region D:310-432 [Jmol] [rasmolscript] [script source]
  • Fold representative 1vyw 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: [1vyw_B] [1vyw] [1vyw_C] [1vyw_A] [1vyw_D]
  • SWISS-PROT database: [P20248] [P24941]
  • Domain organization of [CCNA2_HUMAN] [CDK2_HUMAN] by SWISSPFAM
  • Domains found in 1VYW: [CYCLIN] [Cyclin_C] [S_TKc ] by SMART
  • Other resources with information on 1VYW
  • Community annotation for 1VYW 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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