4NHY Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA) date
authors Horita, S., McDonough, M.A., Schofield, C.J.
compound source
symmetry
R_factor
R_Free 0.2256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.60
ligand GOL, MN, PD2 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases., Horita S, Scotti JS, Thinnes C, Mottaghi-Taromsari YS, Thalhammer A, Ge W, Aik W, Loenarz C, Schofield CJ, McDonough MA, Structure. 2015 Feb 19. pii: S0969-2126(15)00038-6. doi:, 10.1016/j.str.2015.01.014. PMID:25728928
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (646 Kb) [Save to disk]
  • Biological Unit Coordinates (4nhy.pdb1.gz) 163 Kb
  • Biological Unit Coordinates (4nhy.pdb2.gz) 164 Kb
  • Biological Unit Coordinates (4nhy.pdb3.gz) 161 Kb
  • Biological Unit Coordinates (4nhy.pdb4.gz) 164 Kb
  • Biological Unit Coordinates (4nhy.pdb5.gz) 320 Kb
  • Biological Unit Coordinates (4nhy.pdb6.gz) 320 Kb
  • LPC: Ligand-Protein Contacts for 4NHY
  • CSU: Contacts of Structural Units for 4NHY
  • Structure Factors (553 Kb)
  • Retrieve 4NHY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NHY from S2C, [Save to disk]
  • Re-refined 4nhy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NHY 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 4NHY
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4NHY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nhy_A] [4nhy_C] [4nhy_D] [4nhy] [4nhy_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4NHY: [P4Hc ] by SMART
  • Other resources with information on 4NHY
  • Community annotation for 4NHY at PDBWiki (http://pdbwiki.org)

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