3CPW Ribosome date Apr 01, 2008
title The Structure Of The Antibiotic Linezolid Bound To The Large Subunit Of Haloarcula Marismortui
authors J.A.Ippolito, Z.K.Kanyo, D.Wang, F.J.Franceschi, P.B.Moore, T.A.S E.M.Duffy
compound source
Molecule: 23s Ribosomal Rna
Chain
Mutation: Yes
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L2p
Chain: A

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L3p
Chain: B
Synonym: Hmal2, Hl4

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L4p
Chain: C
Synonym: Hmal3, Hl1

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L5p
Chain: D
Synonym: Hmal4, Hl6

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L6p
Chain: E
Synonym: Hmal5, Hl13

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L7ae
Chain: F
Synonym: Hmal6, Hl10

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L10e
Chain: G
Synonym: Hs6

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L10e
Chain: H
Synonym: Ribosomal Protein L10, Acidic Ribosomal Protein P0 L10e, Hmal10;

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L13p
Chain: I

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L14p
Chain: J
Synonym: Hmal13

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L15p
Chain: K
Synonym: Hmal14, Hl27

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L15e
Chain: L
Synonym: Hmal15, Hl9

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L18p
Chain: M
Synonym: 50s Ribosomal Protein Lc12

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L18e
Chain: N
Synonym: Hmal18, Hl12

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L19e
Chain: O
Synonym: Hl29, L19

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L21e
Chain: P
Synonym: Hmal19, Hl24

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L22p
Chain: Q
Synonym: Hl31

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L23p
Chain: R
Synonym: Hmal22, Hl23

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L24p
Chain: S
Synonym: Hmal23, Hl25, L21

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L24e
Chain: T
Synonym: Hmal24, Hl16, Hl15

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L29p
Chain: U
Synonym: Hl21hl22

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L30p
Chain: V
Synonym: Hmal29, Hl33

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L31e
Chain: W
Synonym: Hmal30, Hl20, Hl16

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L32e
Chain: X
Synonym: L34, Hl30

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L37ae
Chain: Y
Synonym: Hl5

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L37e
Chain: Z

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L39e
Chain: 1
Synonym: L35e

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 50s Ribosomal Protein L44e
Chain: 2
Synonym: Hl39e, Hl46e

Organism_scientific: Haloarcula Marismortui
Organism_common: Halobacterium Marismortui
Organism_taxid: 2238
Strain: Dt41

Molecule: 5'-R(Cpcpap(Phe)(Aca))-3'
Chain: 4
Synonym: La, Hla
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.191 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
211.730 298.580 575.290 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand ACE, CD, CL, K, MG, NA, SR, ZLD enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


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 referenceCrystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit., Ippolito JA, Kanyo ZF, Wang D, Franceschi FJ, Moore PB, Steitz TA, Duffy EM, J Med Chem. 2008 Jun 26;51(12):3353-6. PMID:18494460
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2004 Kb) [Save to disk]
  • Biological Unit Coordinates (3cpw.pdb1.gz) 1964 Kb
  • LPC: Ligand-Protein Contacts for 3CPW
  • CSU: Contacts of Structural Units for 3CPW
  • Likely Quarternary Molecular Structure file(s) for 3CPW
  • Structure Factors (3683 Kb)
  • Retrieve 3CPW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CPW from S2C, [Save to disk]
  • Re-refined 3cpw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CPW 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 3CPW
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3CPW, from MSDmotif at EBI
  • Fold representative 3cpw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cpw_T] [3cpw_1] [3cpw_4] [3cpw_E] [3cpw_K] [3cpw_V] [3cpw_O] [3cpw_F] [3cpw_I] [3cpw_X] [3cpw_S] [3cpw_J] [3cpw_9] [3cpw_M] [3cpw_P] [3cpw_L] [3cpw_D] [3cpw_A] [3cpw] [3cpw_N] [3cpw_Y] [3cpw_R] [3cpw_Q] [3cpw_0] [3cpw_G] [3cpw_U] [3cpw_H] [3cpw_Z] [3cpw_W] [3cpw_C] [3cpw_B] [3cpw_2]
  • SWISS-PROT database: [P60617] [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] [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 3CPW: [HhH1] [KOW] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART
  • Other resources with information on 3CPW
  • Community annotation for 3CPW at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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