4OHY

C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate bound state)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.182

Literature

Macromolecules
Sequence Display for 4OHY

Classification: RNA BINDING PROTEIN / RNA

Total Structure Weight: 49486.87


Macromolecule Entities
Molecule Chains Length Organism Details
Protein clpf-1 A 431 Caenorhabditis elegans Gene Name(s): clpf-1 F59A2.4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*GP*C)-3') B 2 synthetic diribonucleotide GC

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

A PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
2PE
Query on 2PE

A NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.182
  • Space Group: P 31

Unit Cell:

Length (Å) Angle (°)
a = 100.43 α = 90.00
b = 100.43 β = 90.00
c = 40.33 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-01-18
  • Released Date: 2014-05-14
  • Deposition author(s): Dikfidan, A., Loll, B., Zeymer, C., Clausen, T., Meinhart, A.

Revision History

  • Version 1_0: 2014-05-14

    Type: Initial release

  • Version 1_1: 2014-07-02

    Type: Database references

  • Version 1_2: 2015-01-21

    Type: Structure summary

  • Version 1_3: 2017-11-22

    Type: Refinement description