5DIR Hydrolase date Sep 01, 2015
title Membrane Protein At 2.8 Angstroms
authors L.Vogeley, T.El Arnaout, J.Bailey, C.Boland, M.Caffrey
compound source
Molecule: Lipoprotein Signal Peptidase
Chain: A, B, C, D
Synonym: Prolipoprotein Signal Peptidase,Signal Peptidase I II;
Ec: 3.4.23.36
Engineered: Yes
Other_details: N-Terminal 6xhis Tag And Thrombin Site
Organism_scientific: Pseudomonas Aeruginosa (Strain Atcc 15 Pao1 1c Prs 101 Lmg 12228);
Organism_taxid: 208964
Strain: Atcc 15692 Pao1 1c Prs 101 Lmg 12228
Gene: Lspa, Ls, Pa4559
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: C41
Expression_system_plasmid: Pet28a

Molecule: Globomycin
Chain: E, F, G, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.219 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.480 105.880 85.390 90.00 96.92 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 5BV, ALO, IIL, MLE, OLC enzyme Hydrolase E.C.3.4.23.36 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural basis of lipoprotein signal peptidase II action and inhibition by the antibiotic globomycin., Vogeley L, El Arnaout T, Bailey J, Stansfeld PJ, Boland C, Caffrey M, Science. 2016 Feb 19;351(6275):876-80. doi: 10.1126/science.aad3747. PMID:26912896
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (124 Kb) [Save to disk]
  • Biological Unit Coordinates (5dir.pdb1.gz) 32 Kb
  • Biological Unit Coordinates (5dir.pdb2.gz) 31 Kb
  • Biological Unit Coordinates (5dir.pdb3.gz) 30 Kb
  • Biological Unit Coordinates (5dir.pdb4.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 5DIR
  • CSU: Contacts of Structural Units for 5DIR
  • Structure Factors (430 Kb)
  • Retrieve 5DIR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DIR from S2C, [Save to disk]
  • Re-refined 5dir structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DIR 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 5DIR
  • 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: [5dir_D] [5dir_H] [5dir_F] [5dir_A] [5dir_G] [5dir_C] [5dir_B] [5dir] [5dir_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DIR
  • Community annotation for 5DIR at PDBWiki (http://pdbwiki.org)

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