5IWA Translation date Mar 22, 2016
title Crystal Structure Of The 30s Ribosomal Subunit From Thermus Thermophilus In Complex With The Ge81112 Peptide Antibiotic
authors A.Schedlbauer, T.Kaminishi, B.Ochoa-Lizarralde, N.Chieko, K.Masa C.Takemoto, S.Yokoyama, S.R.Connell, P.Fucini
compound source
Molecule: 30s Ribosomal Protein S2
Chain: B
 Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S3
Chain: C
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S4
Chain: D
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S5
Chain: E
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Ts9
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S7
Chain: G
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S8
Chain: H
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S9
Chain: I
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S10
Chain: J
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S11
Chain: K
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S12
Chain: L
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S13
Chain: M
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S14 Type Z
Chain: N
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S15
Chain: O
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S17
Chain: Q
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S18
Chain: R
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S19
Chain: S
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein S20
Chain: T
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 30s Ribosomal Protein Thx
Chain: V
Synonym: S31
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: 16s Ribosomal Rna
Chain: A
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852
symmetry Space Group: P 41 21 2
R_factor 0.166 R_Free 0.218
crystal
cell
length a length b length c angle alpha angle beta angle gamma
413.140 413.140 173.630 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand 6EK, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


Primary referenceInhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding., Fabbretti A, Schedlbauer A, Brandi L, Kaminishi T, Giuliodori AM, Garofalo R, Ochoa-Lizarralde B, Takemoto C, Yokoyama S, Connell SR, Gualerzi CO, Fucini P, Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2286-95. doi:, 10.1073/pnas.1521156113. Epub 2016 Apr 6. PMID:27071098
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2204 Kb) [Save to disk]
  • Biological Unit Coordinates (5iwa.pdb1.gz) 2184 Kb
  • LPC: Ligand-Protein Contacts for 5IWA
  • CSU: Contacts of Structural Units for 5IWA
  • Structure Factors (2230 Kb)
  • Retrieve 5IWA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5IWA from S2C, [Save to disk]
  • Re-refined 5iwa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5IWA 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 5IWA
  • 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: [5iwa_R] [5iwa_T] [5iwa_O] [5iwa_S] [5iwa_N] [5iwa_C] [5iwa_E] [5iwa_L] [5iwa_Q] [5iwa] [5iwa_F] [5iwa_P] [5iwa_V] [5iwa_K] [5iwa_D] [5iwa_A] [5iwa_G] [5iwa_B] [5iwa_H] [5iwa_M] [5iwa_I] [5iwa_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5IWA: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 5IWA
  • Community annotation for 5IWA at PDBWiki (http://pdbwiki.org)

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