2FDH Oxidoreductase Dna date Dec 14, 2005
title Crystal Structure Of Alkb In Complex With Mn(II), 2-Oxogluta Methylated Trinucleotide T-Mea-T
authors B.Yu, J.Benach, W.C.Edstrom, B.R.Gibney, J.F.Hunt, Northeast Stru Genomics Consortium (Nesg)
compound source
Molecule: 5'-D(Ptp(Ma7)Pt)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Alkylated Dna Repair Protein Alkb
Chain: A
Fragment: Residues 12-216
Engineered: Yes

Organism_scientific: Escherichia Coli K12
Organism_taxid: 83333
Strain: K-12
Gene: Alkb, Aidd
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26
symmetry Space Group: P 43
R_factor 0.187 R_Free 0.228
length a length b length c angle alpha angle beta angle gamma
40.680 40.680 118.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand AKG, MA7, MN enzyme

Primary referenceCrystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB., Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF, Nature. 2006 Feb 16;439(7078):879-84. PMID:16482161
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (2fdh.pdb1.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 2FDH
  • CSU: Contacts of Structural Units for 2FDH
  • Likely Quarternary Molecular Structure file(s) for 2FDH
  • Structure Factors (354 Kb)
  • Retrieve 2FDH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FDH from S2C, [Save to disk]
  • Re-refined 2fdh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2FDH 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 2FDH
  • 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 2FDH, from MSDmotif at EBI
  • Fold representative 2fdh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2fdh_B] [2fdh] [2fdh_A]
  • SWISS-PROT database: [P05050]
  • Domain organization of [ALKB_ECOLI] by SWISSPFAM
  • Other resources with information on 2FDH
  • Community annotation for 2FDH 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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