2F4V Ribosome date Nov 24, 2005
title 30s Ribosome + Designer Antibiotic
authors J.B.Murray, S.O.Meroueh, R.J.Russell, G.Lentzen, J.Haddad, S.Mobashery
compound source
Molecule: 16s Ribosomal Rna
Chain: A
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 5'-R(Pupupcpu)-3'
Chain: Z
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S2
Chain: B
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S3
Chain: C
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S4
Chain: D
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S5
Chain: E
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Ts9
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S7
Chain: G
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S8
Chain: H
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S9
Chain: I
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S10
Chain: J
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S11
Chain: K
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S12
Chain: L
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S13
Chain: M
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S14
Chain: N
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S15
Chain: O
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S17
Chain: Q
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S18
Chain: R
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S19
Chain: S
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S20
Chain: T
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 41 21 2
R_factor 0.259 R_Free 0.315
crystal
cell
length a length b length c angle alpha angle beta angle gamma
403.323 403.323 176.685 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand AB9, D2C, K, 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


Primary referenceInteractions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site., Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S, Chem Biol. 2006 Feb;13(2):129-38. PMID:16492561
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1051 Kb) [Save to disk]
  • Biological Unit Coordinates (2f4v.pdb1.gz) 1029 Kb
  • LPC: Ligand-Protein Contacts for 2F4V
  • CSU: Contacts of Structural Units for 2F4V
  • Likely Quarternary Molecular Structure file(s) for 2F4V
  • Retrieve 2F4V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2F4V from S2C, [Save to disk]
    • View 2F4V 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 2F4V
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2F4V, from MSDmotif at EBI
  • Fold representative 2f4v from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2f4v_E] [2f4v_P] [2f4v_L] [2f4v_S] [2f4v_F] [2f4v_R] [2f4v_Z] [2f4v_H] [2f4v_O] [2f4v_J] [2f4v_K] [2f4v_B] [2f4v_C] [2f4v_I] [2f4v_T] [2f4v_G] [2f4v] [2f4v_M] [2f4v_A] [2f4v_Q] [2f4v_D] [2f4v_N]
  • SWISS-PROT database: [Q5SHN7] [P80376] [Q5SHN3] [P80377] [Q5SHQ1] [Q5SJ76] [Q5SJH3] [Q5SHP7] [Q5SLQ0] [Q5SHP2] [P80380] [P80371] [P80372] [P80373] [Q5SHQ5] [Q5SLP8] [P17291] [Q5SHQ2] [P80374]
  • Domain organization of [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THET8] [RS18_THET8] [RS19_THET8] [RS20_THET8] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET8] by SWISSPFAM
  • Domains found in 2F4V: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 2F4V
  • Community annotation for 2F4V 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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