5L9Q Hydrolase date Jun 10, 2016
title Oceanobacillus Iheyensis Macrodomain With Adp
authors F.Gil-Ortiz, R.Zapata-Perez, A.B.Martinez, J.Juanhuix, A.Sanchez
compound source
Molecule: Macrod-Type Macrodomain
Chain: A, B
Engineered: Yes
 Organism_scientific: Oceanobacillus Iheyensis (Strain Dsm 1 Cip 107618 Jcm 11309 Kctc 3954 Hte831);
Organism_taxid: 221109
Gene: Ob2288
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta 2
Expression_system_vector_type: Pet28a
Expression_system_plasmid: Pet28a-Oimacrod
symmetry Space Group: P 1 21 1
R_factor 0.170 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.342 95.714 54.734 90.00 115.59 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand ADP, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis., Zapata-Perez R, Gil-Ortiz F, Martinez-Monino AB, Garcia-Saura AG, Juanhuix J, Sanchez-Ferrer A, Open Biol. 2017 Apr;7(4). pii: 160327. doi: 10.1098/rsob.160327. PMID:28446708
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (5l9q.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (5l9q.pdb2.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 5L9Q
  • CSU: Contacts of Structural Units for 5L9Q
  • Structure Factors (1435 Kb)
  • Retrieve 5L9Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L9Q from S2C, [Save to disk]
  • Re-refined 5l9q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5L9Q 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 5L9Q
  • 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: [5l9q_A] [5l9q_B] [5l9q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5L9Q
  • Community annotation for 5L9Q at PDBWiki (http://pdbwiki.org)

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