2KMK Dna Binding Protein Dna date Jul 30, 2009
title Gfi-1 Zinc Fingers 3-5 Complexed With Dna
authors S.Lee, Z.Wu
compound source
Molecule: Zinc Finger Protein Gfi-1
Chain: A
Fragment: Unp Residues 312-393
Synonym: Growth Factor Independent Protein 1
Engineered: Yes
 Organism_scientific: Rattus Norvegicus
Organism_common: Brown Rat,Rat,Rats
Organism_taxid: 10116
Gene: Gfi1, Gfi-1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Plyss
Expression_system_vector: Pet17b

Molecule: Dna (5'-D(Cpaptpapapaptpcpapcptpgpcp 3');
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Tpapgpgpcpapgptpgpaptptptp 3');
Chain: C
Engineered: Yes
Synthetic: Yes
methodSolution NMR
ligand ZN enzyme
Primary referenceSolution Structure of Gfi-1 Zinc Domain Bound to Consensus DNA., Lee S, Doddapaneni K, Hogue A, McGhee L, Meyers S, Wu Z, J Mol Biol. 2010 Feb 11. PMID:20153336
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (496 Kb) [Save to disk]
  • Biological Unit Coordinates (2kmk.pdb1.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 2KMK
  • CSU: Contacts of Structural Units for 2KMK
  • Original NMR restraints for 2KMK from PDB
  • Retrieve 2KMK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2KMK from S2C, [Save to disk]
    • View 2KMK 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 2KMK
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2KMK, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2kmk_B] [2kmk] [2kmk_A] [2kmk_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2KMK: [ZnF_C2H2] [ZnF_C2HC ] by SMART
    • Other resources with information on 2KMK
  • Community annotation for 2KMK 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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