3PIP Ribosome Antibiotic date Nov 07, 2010
title Crystal Structure Of The Synergistic Antibiotic Pair Lankamy Lankacidin In Complex With The Large Ribosomal Subunit
authors M.J.Belousoff, T.Shapira, A.Bashan, E.Zimmerman, H.Kinashi, H.Roz A.Yonath
compound source
Molecule: Ribosomal 23s Rna
Chain: X
Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 5s Ribosomal Rna
Chain: Y

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

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
Synonym: General Stress Protein Ctc

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 0.257 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
169.723 408.562 693.334 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.45 Å
ligand K, LC2, LMA, MG, NA 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 referenceCrystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit., Belousoff MJ, Shapira T, Bashan A, Zimmerman E, Rozenberg H, Arakawa K, Kinashi H, Yonath A, Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2717-22. Epub 2011 Jan 31. PMID:21282615
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3616 Kb) [Save to disk]
  • Biological Unit Coordinates (3pip.pdb1.gz) 3600 Kb
  • LPC: Ligand-Protein Contacts for 3PIP
  • CSU: Contacts of Structural Units for 3PIP
  • Structure Factors (3535 Kb)
  • Retrieve 3PIP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PIP from S2C, [Save to disk]
  • Re-refined 3pip structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PIP 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 3PIP
  • 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 3PIP, from MSDmotif at EBI
  • Fold representative 3pip from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pip_V] [3pip_H] [3pip_Y] [3pip_R] [3pip_O] [3pip_X] [3pip_1] [3pip_T] [3pip_E] [3pip_S] [3pip_D] [3pip_K] [3pip_A] [3pip_W] [3pip_I] [3pip_L] [3pip_B] [3pip_P] [3pip_M] [3pip_4] [3pip_3] [3pip_J] [3pip_N] [3pip_Z] [3pip_U] [3pip] [3pip_C] [3pip_Q] [3pip_F] [3pip_2] [3pip_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PIP: [KOW] [RL11] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C ] by SMART
  • Other resources with information on 3PIP
  • Community annotation for 3PIP 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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