2WDI Ribosome date Mar 24, 2009
title Structure Of The Thermus Thermophilus 70s Ribosome In Complex With Mrna, Paromomycin, Acylated A-Site Trna, Deacylated P-Site Trna, And E-Site Trna. This File Contains The 50s Subunit For Molecule I.
authors R.M.Voorhees, A.Weixlbaumer, D.Loakes, A.C.Kelley, V.Ramakrishnan
compound source
Molecule: 23s Ribosomal Rna
Chain: A
Other_details: Chain A (23s Rna) Has E.Coli Residue Numbering, Based On A Structural Alignment With The Corresponding E. Coli Structure In 2aw4;
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 5s Ribosomal Rna
Chain: B

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L1
Chain: C

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L2
Chain: D

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L3
Chain: E

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L4
Chain: F

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L5
Chain: G

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L6
Chain: H

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L9
Chain: I

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L13
Chain: N

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L14
Chain: O

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L15
Chain: P

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L16
Chain: Q

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L17
Chain: R

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L18
Chain: S

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L19
Chain: T

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L20
Chain: U

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L21
Chain: V

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L22
Chain: W

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L23
Chain: X

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L24
Chain: Y

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L25
Chain: Z

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L27
Chain

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L28
Chain: 1

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L29
Chain: 2

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L30
Chain: 3

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L31
Chain: 4

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L32
Chain: 5

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L33
Chain: 6

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L34
Chain: 7

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L35
Chain: 8

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: 50s Ribosomal Protein L36
Chain: 9

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 21 21 21
R_factor 0.2230 R_Free 0.2717
crystal
cell
length a length b length c angle alpha angle beta angle gamma
212.132 450.802 629.616 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.30 Å
Gene
Ontology
ChainFunctionProcessComponent
4


6


7, 2, 1, 0, 3, 8, 5


9


C


D


E


F


G


H


I


N


O


P


Q


R


S


T


V


W


X


Y, U


Z


Primary referenceInsights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome., Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V, Nat Struct Mol Biol. 2009 Apr 12. PMID:19363482
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1682 Kb) [Save to disk]
  • Biological Unit Coordinates (2wdi.pdb1.gz) 1659 Kb
  • CSU: Contacts of Structural Units for 2WDI
  • Likely Quarternary Molecular Structure file(s) for 2WDI
  • Structure Factors (9680 Kb)
  • Retrieve 2WDI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2WDI from S2C, [Save to disk]
  • View 2WDI 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 2WDI
  • 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 2WDI, from MSDmotif at EBI
  • Fold representative 2wdi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2wdi_0] [2wdi_O] [2wdi_X] [2wdi_C] [2wdi_1] [2wdi_G] [2wdi_7] [2wdi_Q] [2wdi_3] [2wdi_A] [2wdi_N] [2wdi_S] [2wdi_I] [2wdi_R] [2wdi_2] [2wdi_5] [2wdi_8] [2wdi_H] [2wdi_F] [2wdi_P] [2wdi_6] [2wdi_9] [2wdi_E] [2wdi_Y] [2wdi_U] [2wdi_W] [2wdi] [2wdi_V] [2wdi_4] [2wdi_B] [2wdi_T] [2wdi_D] [2wdi_Z]
  • SWISS-PROT database: [P60488] [Q5SHP8] [Q5SHQ7] [P60489] [Q9Z9H5] [Q5SHQ4] [P60490] [Q5SLP7] [P60491] [P60492] [Q5SHP3] [Q5SHP0] [Q5SHP9] [Q5SHZ1] [P60493] [P60494] [Q5SHP6] [P60405] [Q5SHQ6] [Q5SJE1] [P80339] [P35871] [P80340] [Q5SKU1] [Q5SHR2] [Q5SHN8] [Q5SHN9] [Q5SHQ0] [Q5SHQ3] [Q5SLQ1]
  • Domain organization of [RL13_THET8] [RL14_THET8] [RL15_THET8] [RL16_THET8] [RL17_THET8] [RL18_THET8] [RL19_THET8] [RL1_THET8] [RL20_THET8] [RL21_THET8] [RL22_THET8] [RL23_THET8] [RL24_THET8] [RL25_THET8] [RL27_THET8] [RL28_THET8] [RL29_THET8] [RL2_THET8] [RL30_THET8] [RL31_THET8] [RL32_THET8] [RL33_THET8] [RL34_THET8] [RL35_THET8] [RL36_THET8] [RL3_THET8] [RL4_THET8] [RL5_THET8] [RL6_THET8] [RL9_THET8] by SWISSPFAM
  • Domain found in 2WDI: [KOW ] by SMART
  • Other resources with information on 2WDI
  • Community annotation for 2WDI 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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