1YIT Ribosome Antibiotic date Jan 13, 2005
title Crystal Structure Of Virginiamycin M And S Bound To The 50s Subunit Of Haloarcula Marismortui
authors D.Tu, G.Blaha, P.B.Moore, T.A.Steitz
compound source
Molecule: 23s Ribosomal Rna
Chain
Engineered: Yes
Other_details: Encoded By Rrna Operon
 Synthetic: Yes

Molecule: 50s Ribosomal Protein L37e
Chain: 1
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L39e
Chain: 2
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L44e
Chain: 3
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Virginiamycin S1
Chain: 8
Synonym: Virginiamycin Factor S1, Virginiamycin S
Organism_scientific: Streptomyces Virginiae
Organism_taxid: 1961

Molecule: 5s Ribosomal Rna
Chain: 9
Engineered: Yes
Synthetic: Yes

Molecule: 50s Ribosomal Protein L2p
Chain: A
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L3p
Chain: B
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L4e
Chain: C
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L5p
Chain: D
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L6p
Chain: E
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L7ae
Chain: F
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Acidic Ribosomal Protein P0 Homolog
Chain: G
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: H
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L11p
Chain: I
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L13p
Chain: J
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L14p
Chain: K
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15p
Chain: L
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15e
Chain: M
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18p
Chain: N
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18e
Chain: O
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L19e
Chain: P
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L21e
Chain: Q
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L22p
Chain: R
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L23p
Chain: S
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24p
Chain: T
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24e
Chain: U
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L29p
Chain: V
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L30p
Chain: W
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L31e
Chain: X
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L32e
Chain: Y
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37ae
Chain: Z
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.175 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
212.583 299.758 573.560 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 004, 1MA, CD, CL, DBB, K, MEA, MG, MHV, MHW, NA, OMG, OMU, PSU, UR3, VIR enzyme
related structures by homologous chain: 1M90, 1YI2, 1YJW
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


A


B


C


D


E


F
  • ribonuclease P activity


    • G


    H


    I


    J


    K


    L


    M


    N


    O


    P


    Q


    R


    S


    T


    U


    V


    W


    X


    Y


    Z


    Primary referenceStructures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance., Tu D, Blaha G, Moore PB, Steitz TA, Cell. 2005 Apr 22;121(2):257-70. PMID:15851032
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1833 Kb) [Save to disk]
  • Biological Unit Coordinates (1yit.pdb1.gz) 1805 Kb
  • LPC: Ligand-Protein Contacts for 1YIT
  • CSU: Contacts of Structural Units for 1YIT
  • Likely Quarternary Molecular Structure file(s) for 1YIT
  • Structure Factors (3260 Kb)
  • Retrieve 1YIT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YIT from S2C, [Save to disk]
  • Re-refined 1yit structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YIT 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 1YIT
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1YIT, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yit_I] [1yit_X] [1yit_E] [1yit_J] [1yit_C] [1yit_D] [1yit_W] [1yit_K] [1yit_M] [1yit_H] [1yit_U] [1yit_O] [1yit_8] [1yit_9] [1yit_0] [1yit_A] [1yit_2] [1yit_G] [1yit_N] [1yit_L] [1yit_T] [1yit_Y] [1yit_Q] [1yit_R] [1yit_Z] [1yit_3] [1yit_S] [1yit_P] [1yit_F] [1yit_1] [1yit_B] [1yit] [1yit_V]
  • SWISS-PROT database: [P60617] [P14122] [P29198] [P22450] [P60618] [P12737] [P12733] [P14123] [P14119] [P12734] [P10970] [P12732] [P14116] [P10972] [P10971] [P20276] [P14121] [P18138] [P12736] [P60619] [P32410] [P22452] [P20279] [P32411] [P12735] [P14124] [P14135] [P12743] [P15825]
  • Domain organization of [RL10_HALMA] [RL11_HALMA] [RL13_HALMA] [RL14_HALMA] [RL15E_HALMA] [RL15_HALMA] [RL18E_HALMA] [RL18_HALMA] [RL19_HALMA] [RL21_HALMA] [RL22_HALMA] [RL23_HALMA] [RL24E_HALMA] [RL24_HALMA] [RL29_HALMA] [RL2_HALMA] [RL30_HALMA] [RL31_HALMA] [RL32_HALMA] [RL37A_HALMA] [RL37_HALMA] [RL39_HALMA] [RL3_HALMA] [RL44_HALMA] [RL4_HALMA] [RL5_HALMA] [RL6_HALMA] [RL7A_HALMA] [RLA0_HALMA] by SWISSPFAM
  • Domains found in 1YIT: [HhH1] [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
    • Other resources with information on 1YIT
  • Community annotation for 1YIT 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