1XBP Ribosome date Aug 31, 2004
title Inhibition Of Peptide Bond Formation By Pleuromutilins: The Of The 50s Ribosomal Subunit From Deinococcus Radiodurans I With Tiamulin
authors F.Schluenzen, E.Pyetan, P.Fucini, A.Yonath, J.M.Harms
compound source
Molecule: 23s Ribosomal Rna
Chain
 Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 5s Ribosomal Rna
Chain: 9
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 L9
Chain: F
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L11
Chain: G
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L13
Chain: H
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L14
Chain: I
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L15
Chain: J
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: Ribosomal Protein L16
Chain: K
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L17
Chain: L
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L18
Chain: M
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L19
Chain: N
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L20
Chain: O
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L21
Chain: P
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L22
Chain: Q
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L23
Chain: R
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L24
Chain: S
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L25
Chain: T
Synonym: General Stress Protein Ctc
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L27
Chain: U
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L29
Chain: W
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L30
Chain: X
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L31
Chain: Y
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 0.290 R_Free 0.360
crystal
cell
length a length b length c angle alpha angle beta angle gamma
168.700 405.000 693.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand MUL 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


W


X


Y


Z


Primary referenceInhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin., Schlunzen F, Pyetan E, Fucini P, Yonath A, Harms JM, Mol Microbiol 2004 Dec;54(5):1287-94. PMID:15554968
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1121 Kb) [Save to disk]
  • Biological Unit Coordinates (1xbp.pdb1.gz) 1113 Kb
  • LPC: Ligand-Protein Contacts for 1XBP
  • CSU: Contacts of Structural Units for 1XBP
  • Likely Quarternary Molecular Structure file(s) for 1XBP
  • Retrieve 1XBP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XBP from S2C, [Save to disk]
    • View 1XBP 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 1XBP
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1XBP, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xbp_0] [1xbp_T] [1xbp_P] [1xbp_K] [1xbp_1] [1xbp_B] [1xbp_J] [1xbp_R] [1xbp_L] [1xbp_G] [1xbp_A] [1xbp_M] [1xbp_3] [1xbp_D] [1xbp_N] [1xbp_C] [1xbp_U] [1xbp_Z] [1xbp_H] [1xbp_S] [1xbp_Q] [1xbp_2] [1xbp_F] [1xbp_O] [1xbp] [1xbp_I] [1xbp_E] [1xbp_9] [1xbp_X] [1xbp_4] [1xbp_Y] [1xbp_W]
  • SWISS-PROT database: [Q9RSS7] [Q9RXY1] [Q9RXJ2] [Q9RSK9] [Q9RXJ5] [Q9RSJ5] [Q9RSL2] [Q9RWB4] [Q9RSW7] [Q9RY64] [Q9RXJ7] [Q9RXK0] [Q9RXJ1] [Q9RX88] [Q9RY65] [Q9RXJ4] [Q9RXJ9] [Q9RSL0] [Q9RW44] [P49228] [Q9RSS4] [Q9RSH2] [Q9RSW6] [Q9RSK0] [Q9RXK2] [Q9RXK1] [Q9RXJ0] [Q9RSL3] [Q9RY49]
  • 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] [RL29_DEIRA] [RL2_DEIRA] [RL30_DEIRA] [RL31_DEIRA] [RL32_DEIRA] [RL33_DEIRA] [RL34_DEIRA] [RL35_DEIRA] [RL36_DEIRA] [RL3_DEIRA] [RL4_DEIRA] [RL5_DEIRA] [RL6_DEIRA] [RL9_DEIRA] by SWISSPFAM
  • Domains found in 1XBP: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
    • Other resources with information on 1XBP
  • Community annotation for 1XBP at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science