6D2Z Hydrolase Rna date Apr 14, 2018
title Structure Of Human Usb1 With Uridine-Adenosine, Inactive H20
authors Y.Nomura, E.J.Montemayor, S.E.Butcher
compound source
Molecule: U6 Snrna Phosphodiesterase
Chain: A
Synonym: Husb1
Ec: 3.1.4.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Usb1, C16orf57
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-R(Upa)-3')
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.145 R_Free 0.174
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.393 51.045 46.299 90.00 105.88 90.00
method X-Ray Diffractionresolution 1.18 Å
ligand CL enzyme Hydrolase E.C.3.1.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1., Nomura Y, Roston D, Montemayor EJ, Cui Q, Butcher SE, Nucleic Acids Res. 2018 Sep 12. pii: 5095463. doi: 10.1093/nar/gky812. PMID:30215753
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (6d2z.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 6D2Z
  • CSU: Contacts of Structural Units for 6D2Z
  • Structure Factors (1395 Kb)
  • Retrieve 6D2Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D2Z from S2C, [Save to disk]
  • View 6D2Z 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 6D2Z
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d2z_A] [6d2z_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6D2Z
  • Community annotation for 6D2Z at PDBWiki (http://pdbwiki.org)

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