5NRG Ribosome date Apr 23, 2017
title The Crystal Structure Of The Large Ribosomal Subunit Of Stap Aureus In Complex With Rb02
authors A.Yonath, D.Matzov, Z.Eyal, R.Ben Hamou, E.Zimmerman, H.Rozenberg A.Bashan, M.Fridman
compound source
Molecule: 23s Ribosomal Rna
Chain: X
 Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 5s Ribosomal Rna
Chain: Y
Organism_scientific: Staphylococcus Aureus Subsp. Aureus Nc
Organism_taxid: 93061

Molecule: 50s Ribosomal Protein L2
Chain: A
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L3
Chain: B
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L4
Chain: C
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L5
Chain: D
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L6
Chain: E
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L13
Chain: G
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L14
Chain: H
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L15
Chain: I
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L16
Chain: J
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L17
Chain: K
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L18
Chain: L
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L19
Chain: M
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L20
Chain: N
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L21
Chain: O
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L22
Chain: P
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L23
Chain: Q
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L24
Chain: R
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L25
Chain: S
Synonym: General Stress Protein Ctc
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L27
Chain: T
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L29
Chain: V
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L30
Chain: W
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L32
Chain: Z
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L34
Chain: 2
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325

Molecule: 50s Ribosomal Protein L35
Chain: 3
Organism_scientific: Staphylococcus Aureus (Strain Nctc 832
Organism_taxid: 93061
Strain: Nctc 8325
symmetry Space Group: P 65 2 2
R_factor 0.219 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
279.797 279.797 873.274 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.44 Å
ligand 95H, EPE, MG, MN, MPD, SPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
2


3


A


B


C


D


E


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


W


Z


Primary referenceStructural insights of lincosamides targeting the ribosome of Staphylococcus aureus., Matzov D, Eyal Z, Benhamou RI, Shalev-Benami M, Halfon Y, Krupkin M, Zimmerman E, Rozenberg H, Bashan A, Fridman M, Yonath A, Nucleic Acids Res. 2017 Sep 29;45(17):10284-10292. doi: 10.1093/nar/gkx658. PMID:28973455
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1662 Kb) [Save to disk]
  • Biological Unit Coordinates (5nrg.pdb1.gz) 1639 Kb
  • LPC: Ligand-Protein Contacts for 5NRG
  • CSU: Contacts of Structural Units for 5NRG
  • Structure Factors (6173 Kb)
  • Retrieve 5NRG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NRG from S2C, [Save to disk]
    • View 5NRG 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 5NRG
  • 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: [5nrg_A] [5nrg_Q] [5nrg_V] [5nrg_X] [5nrg_3] [5nrg_I] [5nrg_W] [5nrg_M] [5nrg_Y] [5nrg_O] [5nrg_J] [5nrg_S] [5nrg_B] [5nrg_2] [5nrg_L] [5nrg_D] [5nrg_Z] [5nrg_C] [5nrg_R] [5nrg_G] [5nrg_P] [5nrg_E] [5nrg_T] [5nrg_H] [5nrg_K] [5nrg_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5NRG
  • Community annotation for 5NRG at PDBWiki (http://pdbwiki.org)

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