5XSP Hydrolase date Jun 15, 2017
title The Catalytic Domain Of Gdpp With 5'-Papa
authors F.Wang, L.Gu
compound source
Molecule: Phosphodiesterase Acting On Cyclic Dinucleotides
Chain: A, B
Fragment: Unp Residues 322-661
Engineered: Yes
Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Cdnd, Bn1321_430104
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.197 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.619 117.263 127.368 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand A, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase., Wang F, He Q, Su K, Wei T, Xu S, Gu L, Biochem J. 2018 Jan 5;475(1):191-205. doi: 10.1042/BCJ20170739. PMID:29203646
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (5xsp.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 5XSP
  • CSU: Contacts of Structural Units for 5XSP
  • Structure Factors (737 Kb)
  • Retrieve 5XSP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XSP from S2C, [Save to disk]
  • View 5XSP 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 5XSP
  • 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: [5xsp_A] [5xsp_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XSP
  • Community annotation for 5XSP at PDBWiki (http://pdbwiki.org)

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