1IBK Ribosome date Mar 28, 2001
title Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotic Paromomycin
authors J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan
compound source
Molecule: 16s Ribosomal Rna
Chain: A
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: P-Site Messenger Rna Fragment
Chain: X

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S2
Chain: B

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S3
Chain: C

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S4
Chain: D

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S5
Chain: E

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S6
Chain: F

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S7
Chain: G

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S8
Chain: H

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S9
Chain: I

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S10
Chain: J

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S11
Chain: K

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S12
Chain: L

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S13
Chain: M

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S14
Chain: N

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S15
Chain: O

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S16
Chain: P

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S17
Chain: Q

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S18
Chain: R

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S19
Chain: S

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S20
Chain: T

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein Thx
Chain: V

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 41 21 2
R_factor 0.229 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
401.160 401.160 176.360 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.31 Å
ligand MG, PAR, ZN enzyme
note 1IBK (Molecule of the Month:pdb146)
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


Primary referenceRecognition of cognate transfer RNA by the 30S ribosomal subunit., Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V, Science 2001 May 4;292(5518):897-902. PMID:11340196
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (954 Kb) [Save to disk]
  • Biological Unit Coordinates (1ibk.pdb1.gz) 936 Kb
  • LPC: Ligand-Protein Contacts for 1IBK
  • CSU: Contacts of Structural Units for 1IBK
  • Likely Quarternary Molecular Structure file(s) for 1IBK
  • Structure Factors (1712 Kb)
  • Retrieve 1IBK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IBK from S2C, [Save to disk]
  • Re-refined 1ibk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1IBK 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 1IBK
  • 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 1IBK, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ibka_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ibkb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ibkc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ibkd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1ibke_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1ibkf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1ibkg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1ibkh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1ibki_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1ibkj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1ibkk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1ibkl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1ibkm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1ibkn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1ibko_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1ibkp_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1ibkq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1ibkr_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1ibks_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1ibkt_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1ibkv_, region V [Jmol] [rasmolscript] [script source]
  • Fold representative 1ibk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ibk_N] [1ibk] [1ibk_O] [1ibk_G] [1ibk_A] [1ibk_H] [1ibk_Q] [1ibk_K] [1ibk_B] [1ibk_X] [1ibk_C] [1ibk_F] [1ibk_E] [1ibk_S] [1ibk_J] [1ibk_T] [1ibk_I] [1ibk_V] [1ibk_M] [1ibk_R] [1ibk_P] [1ibk_D] [1ibk_L]
  • SWISS-PROT database: [Q5SHN7] [P80376] [Q5SHN3] [P80377] [Q5SHQ1] [Q5SJ76] [Q5SJH3] [Q5SHP7] [Q5SLQ0] [Q5SHP2] [P80380] [P80371] [P80372] [P80373] [Q5SHQ5] [Q5SLP8] [P17291] [Q5SHQ2] [P80374] [Q5SIH3]
  • Domain organization of [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THET8] [RS18_THET8] [RS19_THET8] [RS20_THET8] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET8] [RSHX_THET8] by SWISSPFAM
  • Domains found in 1IBK: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 1IBK
  • Community annotation for 1IBK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1IBK from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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