3PIO Ribosome Antibiotic date Nov 07, 2010
title Crystal Structure Of The Synergistic Antibiotic Pair Lankamy Lankacidin In Complex With The Large Ribosomal Subunit
authors M.J.Belousoff, T.Shapira, A.Bashan, E.Zimmerman, K.Arakawa, H.Kin H.Rozenberg, A.Yonath
compound source
Molecule: Ribosomal 23s Rna
Chain: X
Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 5s Ribosomal Rna
Chain: Y

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L2
Chain: A

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L3
Chain: B

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L4
Chain: C

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L5
Chain: D

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L6
Chain: E

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L11
Chain: F

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L13
Chain: G

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L14
Chain: H

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L15
Chain: I

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L16
Chain: J

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L17
Chain: K

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L18
Chain: L

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L19
Chain: M

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L20
Chain: N

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L21
Chain: O

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L22
Chain: P

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L23
Chain: Q

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L24
Chain: R

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L25
Chain: S
Synonym: General Stress Protein Ctc

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L27
Chain: T

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L28
Chain: U

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L29
Chain: V

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L30
Chain: W

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L32
Chain: Z

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L33
Chain: 1

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L34
Chain: 2

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L35
Chain: 3

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L36
Chain: 4

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
symmetry Space Group: I 2 2 2
R_factor 0.252 R_Free 0.294
crystal
cell
length a length b length c angle alpha angle beta angle gamma
170.590 410.204 695.078 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.25 Å
ligand K, LMA, MG, NA enzyme
note 3PIO is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


4


A


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


Z


Primary referenceCrystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit., Belousoff MJ, Shapira T, Bashan A, Zimmerman E, Rozenberg H, Arakawa K, Kinashi H, Yonath A, Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2717-22. Epub 2011 Jan 31. PMID:21282615
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3518 Kb) [Save to disk]
  • Biological Unit Coordinates (3pio.pdb1.gz) 3502 Kb
  • LPC: Ligand-Protein Contacts for 3PIO
  • CSU: Contacts of Structural Units for 3PIO
  • Structure Factors (4460 Kb)
  • Retrieve 3PIO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PIO from S2C, [Save to disk]
  • Re-refined 3pio structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PIO 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 3PIO
  • 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 3PIO, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pio_E] [3pio_O] [3pio_I] [3pio_1] [3pio_3] [3pio_J] [3pio_2] [3pio_Z] [3pio_K] [3pio_G] [3pio_W] [3pio] [3pio_B] [3pio_U] [3pio_H] [3pio_D] [3pio_Q] [3pio_4] [3pio_L] [3pio_V] [3pio_R] [3pio_P] [3pio_N] [3pio_A] [3pio_T] [3pio_F] [3pio_M] [3pio_Y] [3pio_S] [3pio_X] [3pio_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PIO: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 3PIO
  • Community annotation for 3PIO 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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