4HUG Hydrolase Dna date Nov 02, 2012
title Structure Of 5-Chlorouracil Modified A:U Base Pairs
authors A.Patra, M.Egli
compound source
Molecule: Ribonuclease H
Chain: A, B
Synonym: Rnase H
Engineered: Yes
Mutation: Yes
Organism_scientific: Bacillus Halodurans
Organism_taxid: 272558
Strain: Atcc Baa-125 Dsm 18197 Ferm 7344 Jcm 9153 C
Gene: Rnha, Bh0863
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Cpgpcpgpapap(Ucl)P(Ucl)Pcpgp
Chain: C, D, E, F
Engineered: Yes
Other_details: Dickerson Dodecamer Dna, Clu78

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.222
length a length b length c angle alpha angle beta angle gamma
63.829 64.638 116.286 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.64 Å
ligand EDO, GOL, MG, UCL enzyme Hydrolase E.C. BRENDA
A, B

Primary referenceStructure, stability and function of 5-chlorouracil modified A:U and G:U base pairs., Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M, Nucleic Acids Res. 2012 Dec 28. PMID:23275540
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (4hug.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (4hug.pdb2.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 4HUG
  • CSU: Contacts of Structural Units for 4HUG
  • Structure Factors (1735 Kb)
  • Retrieve 4HUG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4HUG from S2C, [Save to disk]
  • Re-refined 4hug structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4HUG 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 4HUG
  • 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 4HUG, from MSDmotif at EBI
  • Fold representative 4hug from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4hug] [4hug_A] [4hug_E] [4hug_D] [4hug_B] [4hug_F] [4hug_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4HUG
  • Community annotation for 4HUG at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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