4NRM Oxidoreductase date Nov 27, 2013
title Crystal Structure Of Human Alkbh5 In Complex With Citrate An
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_common: Human
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 0.203 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.726 56.726 146.315 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.17 Å
ligand ACT, FLC enzyme Oxidoreductase E.C.1.14.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (4nrm.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 4NRM
  • CSU: Contacts of Structural Units for 4NRM
  • Structure Factors (149 Kb)
  • Retrieve 4NRM in mmCIF format [Save to disk]
  • Re-refined 4nrm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NRM 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 4NRM
  • 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 4NRM, from MSDmotif at EBI
  • Fold representative 4nrm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nrm_A] [4nrm]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4NRM
  • Community annotation for 4NRM at PDBWiki (http://pdbwiki.org)

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