3HND Oxidoreductase date May 31, 2009
title Crystal Structure Of Human Ribonucleotide Reductase 1 Bound Effector Ttp And Substrate Gdp
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;
Ec: 1.17.4.1
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 0.180 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.159 115.834 221.305 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.21 Å
ligand GDP, MG, SO4, TTP enzyme Oxidoreductase E.C.1.17.4.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (496 Kb) [Save to disk]
  • Biological Unit Coordinates (3hnd.pdb1.gz) 487 Kb
  • LPC: Ligand-Protein Contacts for 3HND
  • CSU: Contacts of Structural Units for 3HND
  • Structure Factors (240 Kb)
  • Retrieve 3HND in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HND from S2C, [Save to disk]
  • Re-refined 3hnd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HND 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 3HND
  • 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 3HND, from MSDmotif at EBI
  • Fold representative 3hnd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hnd] [3hnd_B] [3hnd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3HND
  • Community annotation for 3HND 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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