1PKD Transferase Cell Cycle date Jun 05, 2003
title The Crystal Structure Of Ucn-01 In Complex With Phospho-Cdk2
authors L.N.Johnson, E.De Moliner, N.R.Brown, H.Song
compound source
Molecule: Cell Division Protein Kinase 2
Chain: A, C
Synonym: P33 Protein Kinase
Ec: 2.7.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdk2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex 6p

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ccna2 Or Ccna Or Ccn1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834pet21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21d
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.620 134.570 147.970 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand TPO, UCN BindingDB enzyme Transferase E.C.2.7.1 BRENDA
related structures by homologous chain: 1FIN, 1PXJ, 1VYW
Gene
Ontology
ChainFunctionProcessComponent
A, C


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (195 Kb) [Save to disk]
  • Biological Unit Coordinates (1pkd.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (1pkd.pdb2.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 1PKD
  • CSU: Contacts of Structural Units for 1PKD
  • Likely Quarternary Molecular Structure file(s) for 1PKD
  • Structure Factors (794 Kb)
  • Retrieve 1PKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PKD from S2C, [Save to disk]
  • Re-refined 1pkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PKD 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 1PKD
  • 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 1PKD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pkda_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1pkdb1, region B:175-309 [Jmol] [rasmolscript] [script source]
        - Domain d1pkdb2, region B:310-432 [Jmol] [rasmolscript] [script source]
        - Domain d1pkdc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1pkdd1, region D:175-309 [Jmol] [rasmolscript] [script source]
        - Domain d1pkdd2, region D:310-432 [Jmol] [rasmolscript] [script source]
  • Fold representative 1pkd 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: [1pkd_B] [1pkd_D] [1pkd_A] [1pkd] [1pkd_C]
  • SWISS-PROT database: [P20248] [P24941]
  • Domain organization of [CCNA2_HUMAN] [CDK2_HUMAN] by SWISSPFAM
  • Domains found in 1PKD: [CYCLIN] [Cyclin_C] [S_TKc ] by SMART
  • Other resources with information on 1PKD
  • Community annotation for 1PKD 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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