4NJ4 Oxidoreductase Oxidoreductase Inhibitor date Nov 08, 2013
title Crystal Structure Of Human Alkbh5
authors W.S.Aik, M.A.Mcdonough, C.J.Schofield
compound source
Molecule: Rna Demethylase Alkbh5
Chain: A, B
Fragment: Alkbh5 Residues 66-292
Synonym: Alkylated Dna Repair Protein Alkb Homolog 5, Alpha Ketoglutarate-Dependent Dioxygenase Alkb Homolog 5;
Ec: 1.14.11.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Abh5, Alkbh5, Ofoxd1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 2 21 21
R_factor 0.165 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.100 82.660 89.171 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.02 Å
ligand GOL, MN, NO3, UN9 enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation., Aik W, Scotti JS, Choi H, Gong L, Demetriades M, Schofield CJ, McDonough MA, Nucleic Acids Res. 2014 Apr 1;42(7):4741-54. doi: 10.1093/nar/gku085. Epub 2014, Jan 30. PMID:24489119
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]
  • Biological Unit Coordinates (4nj4.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (4nj4.pdb2.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 4NJ4
  • CSU: Contacts of Structural Units for 4NJ4
  • Structure Factors (398 Kb)
  • Retrieve 4NJ4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NJ4 from S2C, [Save to disk]
  • Re-refined 4nj4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NJ4 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 4NJ4
  • 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 4NJ4, from MSDmotif at EBI
  • Fold representative 4nj4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nj4_B] [4nj4] [4nj4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4NJ4
  • Community annotation for 4NJ4 at PDBWiki (http://pdbwiki.org)

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