4IOA Ribosome Ribosome Inhibitor date Jan 07, 2013
title Crystal Structure Of Compound 4e Bound To Large Ribosomal Su (50s) From Deinococcus Radiodurans
authors S.Han, E.S.Marr
compound source
Molecule: 23s Ribosomal Rna
Chain: X
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 5s Ribosomal Rna
Chain: Y

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 L11
Chain: F

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L13
Chain: G

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L14
Chain: H

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L15
Chain: I

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L16
Chain: J

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L17
Chain: K

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L18
Chain: L

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L19
Chain: M

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L20
Chain: N

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L21
Chain: O

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L22
Chain: P

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L23
Chain: Q

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L24
Chain: R

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L25
Chain: S

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L27
Chain: T

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L28
Chain: U

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L29
Chain: V

Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299

Molecule: 50s Ribosomal Protein L30
Chain: W

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 0.197 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
169.767 406.661 696.738 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand 1F3, MG 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


V


W


Z


Primary referenceNovel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates., Magee TV, Han S, McCurdy SP, Nguyen TT, Granskog K, Marr ES, Maguire BA, Huband MD, Chen JM, Subashi TA, Shanmugasundaram V, Bioorg Med Chem Lett. 2013 Mar 15;23(6):1727-31. doi: 10.1016/j.bmcl.2013.01.067., Epub 2013 Jan 26. PMID:23414806
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1663 Kb) [Save to disk]
  • Biological Unit Coordinates (4ioa.pdb1.gz) 1651 Kb
  • LPC: Ligand-Protein Contacts for 4IOA
  • CSU: Contacts of Structural Units for 4IOA
  • Structure Factors (4886 Kb)
  • Retrieve 4IOA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IOA from S2C, [Save to disk]
  • Re-refined 4ioa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IOA 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 4IOA
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4IOA, from MSDmotif at EBI
  • Fold representative 4ioa from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ioa_O] [4ioa_4] [4ioa_K] [4ioa_R] [4ioa_F] [4ioa_V] [4ioa_P] [4ioa_A] [4ioa_J] [4ioa_2] [4ioa_Z] [4ioa_1] [4ioa_M] [4ioa_N] [4ioa_X] [4ioa_W] [4ioa_C] [4ioa_U] [4ioa_I] [4ioa_3] [4ioa_L] [4ioa_S] [4ioa_Y] [4ioa] [4ioa_E] [4ioa_G] [4ioa_Q] [4ioa_D] [4ioa_B] [4ioa_T] [4ioa_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4IOA: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 4IOA
  • Community annotation for 4IOA at PDBWiki (http://pdbwiki.org)

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