4PY5

Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA

Structural Biology Knowledgebase: 4PY5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 4PY5

Classification: Hydrolase / DNA / RNA

Total Structure Weight: 42990.26


Macromolecule Entities
Molecule Chains Length Organism Details
Ribonuclease A 271 Thermovibrio ammonificans EC#: 3.1.26 IUBMB
Mutation: D78N
Gene Name(s): Theam_0945
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3' B 19 synthetic
5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*C)-3' C 19 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, C SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-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: 2.1 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.183
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.45 α = 90.00
b = 67.66 β = 90.00
c = 107.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-03-26
  • Released Date: 2014-07-30
  • Deposition author(s): Figiel, M., Nowotny, M.

Revision History

  • 2014-10-29
    Type: Entry title | Details: --
  • 2014-08-27
    Type: Citation | Details: Citation update