3HNF Oxidoreductase date May 31, 2009
title Crystal Structure Of Human Ribonucleotide Reductase 1 Bound Effectors Ttp And Datp
authors J.W.Fairman, S.R.Wijerathna, H.Xu, C.G.Dealwis
compound source
Molecule: Ribonucleoside-Diphosphate Reductase Large Subuni
Chain: A, B
Synonym: Ribonucleoside-Diphosphate Reductase Subunit M1, Ribonucleotide Reductase Large Subunit;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rr1, Rrm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21
symmetry Space Group: P 21 21 21
R_factor 0.185 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
68.856 114.388 220.003 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.16 Å
ligand DTP, MG, SO4, TTP enzyme Oxidoreductase E.C. BRENDA
A, B

Primary referenceStructural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization., Fairman JW, Wijerathna SR, Ahmad MF, Xu H, Nakano R, Jha S, Prendergast J, Welin RM, Flodin S, Roos A, Nordlund P, Li Z, Walz T, Dealwis CG, Nat Struct Mol Biol. 2011 Mar;18(3):316-22. Epub 2011 Feb 20. PMID:21336276
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (487 Kb) [Save to disk]
  • Biological Unit Coordinates (3hnf.pdb1.gz) 478 Kb
  • LPC: Ligand-Protein Contacts for 3HNF
  • CSU: Contacts of Structural Units for 3HNF
  • Structure Factors (229 Kb)
  • Retrieve 3HNF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HNF from S2C, [Save to disk]
  • Re-refined 3hnf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HNF 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 3HNF
  • 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 3HNF, from MSDmotif at EBI
  • Fold representative 3hnf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hnf_B] [3hnf_A] [3hnf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3HNF
  • Community annotation for 3HNF at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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