5H4G Hydrolase date Oct 31, 2016
title Structure Of Pin-Domain Protein (Vapc4 Toxin) From Pyrococcu Horikoshii Determined At 1.77 A Resolution
authors A.Biswas, K.Hatti, N.Srinivasan, M.R.N.Murthy, K.Sekar
compound source
Molecule: Ribonuclease Vapc4
Chain: A, B
Synonym: Pin-Domain Protein
Ec: 3.1.-.-
Engineered: Yes
 Organism_scientific: Pyrococcus Horikoshii Ot3
Organism_taxid: 70601
Strain: Ot3
Gene: Vapc4, Ph0500
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.167 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.780 44.640 52.370 90.00 103.40 90.00
method X-Ray Diffractionresolution 1.77 Å
ligand ZN enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • ribonuclease activity


    • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (5h4g.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 5H4G
  • CSU: Contacts of Structural Units for 5H4G
  • Structure Factors (1477 Kb)
  • Retrieve 5H4G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5H4G from S2C, [Save to disk]
  • Re-refined 5h4g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5H4G 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 5H4G
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5h4g_B] [5h4g] [5h4g_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5H4G
  • Community annotation for 5H4G at PDBWiki (http://pdbwiki.org)

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