3DLL Ribosome date Jun 27, 2008
title The Oxazolidinone Antibiotics Perturb The Ribosomal Peptidyl Transferase Center And Effect Trna Positioning
authors D.N.Wilson, F.Schluenzen, J.M.Harms, A.L.Starosta, S.R.Connell, P
compound source
Molecule: Rrna-23s Ribosomal Rna
Chain: X
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: Rrna-5s Ribosomal Rna
Chain: Z

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

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
Synonym: General Stress Protein Ctc

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

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: Y

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 0.259 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
169.700 410.000 695.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand MG, ZLD, ZN enzyme
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


Y


Primary referenceThe oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning., Wilson DN, Schluenzen F, Harms JM, Starosta AL, Connell SR, Fucini P, Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13339-44. Epub 2008 Aug 29. PMID:18757750
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1625 Kb) [Save to disk]
  • Biological Unit Coordinates (3dll.pdb1.gz) 1614 Kb
  • LPC: Ligand-Protein Contacts for 3DLL
  • CSU: Contacts of Structural Units for 3DLL
  • Likely Quarternary Molecular Structure file(s) for 3DLL
  • Structure Factors (3121 Kb)
  • Retrieve 3DLL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DLL from S2C, [Save to disk]
  • Re-refined 3dll structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DLL 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 3DLL
  • 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 3DLL, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dll_O] [3dll_C] [3dll_J] [3dll_Y] [3dll_V] [3dll_I] [3dll_U] [3dll_D] [3dll_Z] [3dll_4] [3dll] [3dll_Q] [3dll_1] [3dll_X] [3dll_H] [3dll_A] [3dll_B] [3dll_W] [3dll_N] [3dll_R] [3dll_3] [3dll_M] [3dll_K] [3dll_T] [3dll_G] [3dll_S] [3dll_F] [3dll_E] [3dll_2] [3dll_L] [3dll_P]
  • SWISS-PROT database: [Q9RSS7] [Q9RXY1] [Q9RXJ2] [Q9RSK9] [Q9RXJ5] [Q9RSJ5] [Q9RSL2] [Q9RWB4] [Q9RSW7] [Q9RY64] [Q9RXJ7] [Q9RXK0] [Q9RXJ1] [Q9RX88] [Q9RY65] [Q9RRG8] [Q9RXJ4] [Q9RXJ9] [Q9RSL0] [P49228] [Q9RSS4] [Q9RSH2] [Q9RSW6] [Q9RSK0] [Q9RXK2] [Q9RXK1] [Q9RXJ0] [Q9RSL3]
  • Domain organization of [RL11_DEIRA] [RL13_DEIRA] [RL14_DEIRA] [RL15_DEIRA] [RL16_DEIRA] [RL17_DEIRA] [RL18_DEIRA] [RL19_DEIRA] [RL20_DEIRA] [RL21_DEIRA] [RL22_DEIRA] [RL23_DEIRA] [RL24_DEIRA] [RL25_DEIRA] [RL27_DEIRA] [RL28_DEIRA] [RL29_DEIRA] [RL2_DEIRA] [RL30_DEIRA] [RL32_DEIRA] [RL33_DEIRA] [RL34_DEIRA] [RL35_DEIRA] [RL36_DEIRA] [RL3_DEIRA] [RL4_DEIRA] [RL5_DEIRA] [RL6_DEIRA] by SWISSPFAM
  • Domains found in 3DLL: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 3DLL
  • Community annotation for 3DLL 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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