4NRO Oxidoreductase date Nov 27, 2013
title Crystal Structure Of Human Alkbh5 In Complex With Alpha-Keto
authors C.Feng, Z.Chen, Y.Liu
compound source
Molecule: Rna Demethylase Alkbh5
Chain: A
Fragment: Unp 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_taxid: 9606
Gene: Abh5, Alkbh5, Ofoxd1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28a
symmetry Space Group: P 43 21 2
R_factor 0.237 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
56.177 56.177 144.940 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand AKG, MN enzyme Oxidoreductase E.C.1.14.11 BRENDA

Primary referenceCrystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition., Feng C, Liu Y, Wang G, Deng Z, Zhang Q, Wu W, Tong Y, Cheng C, Chen Z, J Biol Chem. 2014 Apr 25;289(17):11571-83. doi: 10.1074/jbc.M113.546168. Epub, 2014 Mar 10. PMID:24616105
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (4nro.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 4NRO
  • CSU: Contacts of Structural Units for 4NRO
  • Structure Factors (128 Kb)
  • Retrieve 4NRO in mmCIF format [Save to disk]
  • Re-refined 4nro structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NRO 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 4NRO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4NRO, from MSDmotif at EBI
  • Fold representative 4nro from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nro_A] [4nro]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4NRO
  • Community annotation for 4NRO at PDBWiki (http://pdbwiki.org)

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