1T7D Hydrolase Antibiotic date May 09, 2004
title Crystal Structure Of Escherichia Coli Type I Signal Peptidas Complex With A Lipopeptide Inhibitor
authors M.Paetzel, J.J.Goodall, M.Kania, R.E.Dalbey, M.G.P.Page
compound source
Molecule: Signal Peptidase I
Chain: A, B
Fragment: Residues 76-324
Synonym: Spase I, Leader Peptidase I
Ec: 3.4.21.89
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Lepb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3d

Molecule: Arylomycin A2
Chain: C, D

Organism_scientific: Streptomyces Tu
Organism_taxid: 1931
symmetry Space Group: P 43 21 2
R_factor 0.230 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.609 69.609 258.466 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.47 Å
ligand 5PG, DAL, DSE, M12 enzyme Hydrolase E.C.3.4.21.89 BRENDA
related structures by homologous chain: 1KN9
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor., Paetzel M, Goodall JJ, Kania M, Dalbey RE, Page MG, J Biol Chem 2004 Jul 16;279(29):30781-90. Epub 2004 May 10. PMID:15136583
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (1t7d.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (1t7d.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 1T7D
  • CSU: Contacts of Structural Units for 1T7D
  • Likely Quarternary Molecular Structure file(s) for 1T7D
  • Structure Factors (220 Kb)
  • Retrieve 1T7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1T7D from S2C, [Save to disk]
  • Re-refined 1t7d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1T7D 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 1T7D
  • 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
  • 3D motif for 1T7D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1t7da_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1t7db_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1t7d_A] [1t7d_C] [1t7d_D] [1t7d_B] [1t7d]
  • SWISS-PROT database: [P00803]
  • Domain organization of [LEP_ECOLI] by SWISSPFAM
  • Other resources with information on 1T7D
  • Community annotation for 1T7D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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