2OTL Ribosome date Feb 08, 2007
title Girodazole Bound To The Large Subunit Of Haloarcula Marismor
authors G.Blaha, S.J.Schroeder, J.Tirado-Rives
compound source
Molecule: 23s Ribosomal Rna
Chain
 Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Encoded By Rrna Operons

Molecule: 5s Ribosomal Rna
Chain: 9
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Other_details: Encoded By Rrna Operons

Molecule: 50s Ribosomal Protein L2p
Chain: A
Synonym: Hmal2, Hl4
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L3p
Chain: B
Synonym: Hmal3, Hl1
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L4p
Chain: C
Synonym: Hmal4, Hl6
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L5p
Chain: D
Synonym: Hmal5, Hl13
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L6p
Chain: E
Synonym: Hmal6, Hl10
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L7ae
Chain: F
Synonym: Hs6
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L10e
Chain: G
Synonym: Ribosomal Protein L10, Acidic Ribosomal Protein P0 L10e, Hmal10;
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 L13p
Chain: J
Synonym: Hmal13
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L14p
Chain: K
Synonym: Hmal14, Hl27
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15p
Chain: L
Synonym: Hmal15, Hl9
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L15e
Chain: M
Synonym: 50s Ribosomal Protein Lc12
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18p
Chain: N
Synonym: Hmal18, Hl12
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L18e
Chain: O
Synonym: Hl29, L19
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L19e
Chain: P
Synonym: Hmal19, Hl24
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L21e
Chain: Q
Synonym: Hl31
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L22p
Chain: R
Synonym: Hmal22, Hl23
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L23p
Chain: S
Synonym: Hmal23, Hl25, L21
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24p
Chain: T
Synonym: Hmal24, Hl16, Hl15
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L24e
Chain: U
Synonym: Hl21hl22
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L29p
Chain: V
Synonym: Hmal29, Hl33
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L30p
Chain: W
Synonym: Hmal30, Hl20, Hl16
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L31e
Chain: X
Synonym: L34, Hl30
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L32e
Chain: Y
Synonym: Hl5
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37ae
Chain: Z
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L37e
Chain: 1
Synonym: L35e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L39e
Chain: 2
Synonym: Hl39e, Hl46e
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L44e
Chain: 3
Synonym: La, Hla
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 50s Ribosomal Protein L11p
Chain: I
Synonym: Hmal11
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.204 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
213.077 300.598 575.055 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 1MA, CD, CL, GIR, K, MG, NA, OMG, OMU, PSU, UR3 enzyme
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 referenceThe Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole., Schroeder SJ, Blaha G, Tirado-Rives J, Steitz TA, Moore PB, J Mol Biol. 2007 Apr 13;367(5):1471-9. Epub 2007 Feb 7. PMID:17321546
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1969 Kb) [Save to disk]
  • Biological Unit Coordinates (2otl.pdb1.gz) 1937 Kb
  • LPC: Ligand-Protein Contacts for 2OTL
  • CSU: Contacts of Structural Units for 2OTL
  • Likely Quarternary Molecular Structure file(s) for 2OTL
  • Structure Factors (4956 Kb)
  • Retrieve 2OTL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OTL from S2C, [Save to disk]
  • Re-refined 2otl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2OTL 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 2OTL
  • 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 2OTL, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2otl_N] [2otl_T] [2otl_W] [2otl_0] [2otl_R] [2otl_1] [2otl_I] [2otl_J] [2otl_A] [2otl_2] [2otl_D] [2otl_K] [2otl_B] [2otl_M] [2otl_9] [2otl_H] [2otl_U] [2otl_Z] [2otl_3] [2otl_G] [2otl_F] [2otl_V] [2otl_C] [2otl_X] [2otl_Q] [2otl_P] [2otl_E] [2otl_L] [2otl_O] [2otl_S] [2otl_Y] [2otl]
  • 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 2OTL: [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 2OTL
  • Community annotation for 2OTL 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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