4S1B Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain in complex with Cyclic-di-AMP date
authors Luo, S., Tong, L.
compound source
symmetry
R_factor
R_Free 0.2024
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.10
ligand 2BA, FE enzyme
Primary referenceAn HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence., Huynh TN, Luo S, Pensinger D, Sauer JD, Tong L, Woodward JJ, Proc Natl Acad Sci U S A. 2015 Jan 12. pii: 201416485. PMID:25583510
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (4s1b.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (4s1b.pdb2.gz) 38 Kb
  • Biological Unit Coordinates (4s1b.pdb3.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 4S1B
  • CSU: Contacts of Structural Units for 4S1B
  • Structure Factors (479 Kb)
  • Retrieve 4S1B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4S1B from S2C, [Save to disk]
  • Re-refined 4s1b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4S1B 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 4S1B
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4S1B, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4s1b_A] [4s1b] [4s1b_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4S1B: [HDc ] by SMART
    • Other resources with information on 4S1B
  • Community annotation for 4S1B at PDBWiki (http://pdbwiki.org)

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