1DM2 Cell Cycle date Dec 13, 1999
title Human Cyclin-Dependent Kinase 2 Complexed With The Inhibitor Hymenialdisine
authors A.M.Thunnissen, S.H.Kim
compound source
Molecule: Cyclin-Dependent Kinase 2
Chain: A
Synonym: Cell Division Protein Kinase 2, P33 Protein Kinase
Ec: 2.7.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Sf9 Cells
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Virus
Expression_system_vector: Baculovirus
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.390 70.670 72.260 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand EDO, HMD enzyme Transferase E.C.2.7.1 BRENDA
related structures by homologous chain: 1B39, 1CKP
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInhibition of cyclin-dependent kinases, GSK-3beta and CK1 by hymenialdisine, a marine sponge constituent., Meijer L, Thunnissen AM, White AW, Garnier M, Nikolic M, Tsai LH, Walter J, Cleverley KE, Salinas PC, Wu YZ, Biernat J, Mandelkow EM, Kim SH, Pettit GR, Chem Biol 2000 Jan;7(1):51-63. PMID:10662688
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (1dm2.pdb1.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 1DM2
  • CSU: Contacts of Structural Units for 1DM2
  • Likely Quarternary Molecular Structure file(s) for 1DM2
  • Retrieve 1DM2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DM2 from S2C, [Save to disk]
  • View 1DM2 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 1DM2
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1DM2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dm2a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1dm2 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: [1dm2] [1dm2_A]
  • SWISS-PROT database: [P24941]
  • Domain organization of [CDK2_HUMAN] by SWISSPFAM
  • Domain found in 1DM2: [S_TKc ] by SMART
  • Other resources with information on 1DM2
  • Community annotation for 1DM2 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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