3CXC Ribosome date Apr 24, 2008
title The Structure Of An Enhanced Oxazolidinone Inhibitor Bound To The 50s Ribosomal Subunit Of H. Marismortui
authors J.A.Ippolito, D.Wang, Z.F.Kanyo, E.M.Duffy
compound source
Molecule: 23s Ribosomal Rna
Chain
Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: 5'-R(Cpcpa)-3'
Chain: 4
Engineered: Yes

Synthetic: Yes

Molecule: Ribosomal Protein L2
Chain: A

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L3
Chain: B

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L4
Chain: C

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L5
Chain: D

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L6
Chain: E

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L7ae
Chain: F

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L10
Chain: G

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L10e
Chain: H

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L13
Chain: I

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L14
Chain: J

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L15
Chain: K

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L15e
Chain: L

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L18
Chain: M

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L18e
Chain: N

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L19e
Chain: O

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L21e
Chain: P

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L22
Chain: Q

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L23
Chain: R

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L24
Chain: S

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L24e
Chain: T

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L29
Chain: U

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L30
Chain: V

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L31e
Chain: W

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L32e
Chain: X

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L37ae
Chain: Y

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L37e
Chain: Z

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L39e
Chain: 1

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238

Molecule: Ribosomal Protein L44e
Chain: 2

Organism_scientific: Haloarcula Marismortui
Organism_taxid: 2238
symmetry Space Group: C 2 2 21
R_factor 0.186 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
213.660 300.710 575.370 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CD, CL, K, MG, NA, SLD enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


A


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Y


Z


Primary referenceDesign at the atomic level: design of biaryloxazolidinones as potent orally active antibiotics., Zhou J, Bhattacharjee A, Chen S, Chen Y, Duffy E, Farmer J, Goldberg J, Hanselmann R, Ippolito JA, Lou R, Orbin A, Oyelere A, Salvino J, Springer D, Tran J, Wang D, Wu Y, Johnson G, Bioorg Med Chem Lett. 2008 Dec 1;18(23):6175-8. Epub 2008 Oct 7. PMID:18947996
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1996 Kb) [Save to disk]
  • Biological Unit Coordinates (3cxc.pdb1.gz) 1961 Kb
  • LPC: Ligand-Protein Contacts for 3CXC
  • CSU: Contacts of Structural Units for 3CXC
  • Likely Quarternary Molecular Structure file(s) for 3CXC
  • Structure Factors (3316 Kb)
  • Retrieve 3CXC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CXC from S2C, [Save to disk]
  • Re-refined 3cxc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CXC 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 3CXC
  • 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 3CXC, from MSDmotif at EBI
  • Fold representative 3cxc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cxc_J] [3cxc_K] [3cxc_B] [3cxc_M] [3cxc_D] [3cxc_A] [3cxc_9] [3cxc_Q] [3cxc_N] [3cxc_S] [3cxc_0] [3cxc_C] [3cxc_L] [3cxc_1] [3cxc_V] [3cxc_X] [3cxc_H] [3cxc_4] [3cxc_T] [3cxc_Y] [3cxc_R] [3cxc_E] [3cxc_2] [3cxc_I] [3cxc_F] [3cxc_U] [3cxc] [3cxc_Z] [3cxc_W] [3cxc_G] [3cxc_O] [3cxc_P]
  • SWISS-PROT database: [P29198] [P22450] [P12737] [P12733] [P14123] [P14119] [P12734] [P10970] [P12732] [P14116] [P10972] [P10971] [P20276] [P14121] [P18138] [P12736] [P32410] [P22452] [P20279] [P32411] [P12735] [P14124] [P14135] [P12743] [P15825]
  • Domain organization of [RL13_HALMA] [RL14_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] [RL37_HALMA] [RL39_HALMA] [RL3_HALMA] [RL44_HALMA] [RL4_HALMA] [RL5_HALMA] [RL6_HALMA] [RL7A_HALMA] [RLA0_HALMA] by SWISSPFAM
  • Domains found in 3CXC: [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 3CXC
  • Community annotation for 3CXC 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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