1Y39

Co-evolution of protein and RNA structures within a highly conserved ribosomal domain

Structural Biology Knowledgebase: 1Y39 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Y39

Classification: STRUCTURAL PROTEIN / RNA

Total Structure Weight: 54935.45


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L11 A, B 76 Geobacillus stearothermophilus Fragment: C-Terminal Domain Of Ribosomal Protein L11
Mutation: S69N
Gene Name(s): rplK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
58 Nucleotide Ribosomal 23S RNA Domain C, D 58 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3CO
Query on 3CO

C, D COBALT (III) ION
Co
JAWGVVJVYSANRY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

C, D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
C, D NON-POLYMER C10 H16 N5 O14 P3 G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.220
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 150.24 α = 90.00
b = 150.24 β = 90.00
c = 62.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-11-24
  • Released Date: 2005-03-22
  • Deposition author(s): Dunstan, M.S., GuhaThakurta, D., Draper, D.E., Conn, G.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update