2FD8	Oxidoreductase Dna	date	Dec 13, 2005
title	Crystal Structure Of Alkb In Complex With Fe(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 0.186 R_Free 0.227
crystal cell	length a length b length c angle alpha angle beta angle gamma 40.746 40.746 118.304 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	AKG, FE2, MA7	enzyme
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal 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] (42 Kb) [Save to disk] Biological Unit Coordinates (2fd8.pdb1.gz) 38 Kb LPC: Ligand-Protein Contacts for 2FD8 CSU: Contacts of Structural Units for 2FD8 Likely Quarternary Molecular Structure file(s) for 2FD8 Structure Factors (541 Kb) Retrieve 2FD8 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2FD8 from S2C, [Save to disk] Re-refined 2fd8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2FD8 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 2FD8

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 3D motif for 2FD8, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2fd8_B] [2fd8_A] [2fd8] SWISS-PROT database: [P05050] Domain organization of [ALKB_ECOLI] by SWISSPFAM

Other resources with information on 2FD8

Community annotation for 2FD8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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