2YKR Ribosome Hydrolase date May 30, 2011
title 30s Ribosomal Subunit With Rsga Bound In The Presence Of Gmp
authors Q.Guo, Y.Yuan, Y.Xu, B.Feng, L.Liu, K.Chen, J.Lei, N.Gao
compound source
Molecule: 16s Rrna
Chain: A
 Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S2
Chain: B
Fragment: Residues 9-226
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S3
Chain: C
Fragment: Residues 2-207
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S4
Chain: D
Fragment: Residues 2-206
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S5
Chain: E
Fragment: Residues 10-159
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S6
Chain: F
Fragment: Residues 1-100
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S7
Chain: G
Fragment: Residues 2-152
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S8
Chain: H
Fragment: Residues 2-130
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S9
Chain: I
Fragment: Residues 4-130
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S10
Chain: J
Fragment: Residues 5-102
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S11
Chain: K
Fragment: Residues 13-129
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S12
Chain: L
Fragment: Residues 2-124
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S13
Chain: M
Fragment: Residues 2-115
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S14
Chain: N
Fragment: Residues 2-101
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S15
Chain: O
Fragment: Residues 2-89
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S17
Chain: Q
Fragment: Residues 4-83
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S18
Chain: R
Fragment: Residues 20-74
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S19
Chain: S
Fragment: Residues 3-81
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S20
Chain: T
Fragment: Residues 3-87
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: 30s Ribosomal Protein S21
Chain: U
Fragment: Residues 4-54
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha

Molecule: Putative Ribosome Biogenesis Gtpase Rsga
Chain: W
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 668369
Strain: Dh5alpha
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet28b
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 9.80 Å
ligand
enzyme Hydrolase E.C.3.6.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O
  • mRNA binding involved in pos...


    • P
  • nuclease activity
  • endonuclease activity
  • endodeoxyribonuclease activi...


    • Q


    R


    S


    T
  • ornithine decarboxylase inhi...


    • U


    W


    Primary referenceStructural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy., Guo Q, Yuan Y, Xu Y, Feng B, Liu L, Chen K, Sun M, Yang Z, Lei J, Gao N, Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13100-5. Epub 2011 Jul 25. PMID:21788480
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (914 Kb) [Save to disk]
  • Biological Unit Coordinates (2ykr.pdb1.gz) 907 Kb
  • CSU: Contacts of Structural Units for 2YKR
  • Retrieve 2YKR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YKR from S2C, [Save to disk]
    • View 2YKR 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 2YKR
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2YKR, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ykr_T] [2ykr_B] [2ykr_G] [2ykr_S] [2ykr_F] [2ykr_H] [2ykr] [2ykr_U] [2ykr_L] [2ykr_O] [2ykr_A] [2ykr_N] [2ykr_E] [2ykr_Q] [2ykr_I] [2ykr_R] [2ykr_C] [2ykr_P] [2ykr_M] [2ykr_J] [2ykr_K] [2ykr_W] [2ykr_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2YKR: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 2YKR
  • Community annotation for 2YKR at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science