5T16

Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.226

Literature

Macromolecules
Sequence Display for 5T16

Classification: hydrolase / rna

Total Structure Weight: 282115.66


Macromolecule Entities
Molecule Chains Length Organism Details
Ribonuclease 3 A, B, I, J 276 Saccharomyces cerevisiae EC#: 3.1.26.3 IUBMB
Fragment: unp residues 184-499
Gene Name(s): RNT1 YMR239C YM9408.01C YM9959.21
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ribonuclease 3 C, D, E..., F, K, L, M, NC, D, E, F, K, L, M, N 119 Saccharomyces cerevisiae EC#: 3.1.26.3 IUBMB
Fragment: unp residues 41-199
Gene Name(s): RNT1 YMR239C YM9408.01C YM9959.21
Macromolecule Entities
Molecule Chains Length Organism Details
RNA substrate analog G, H, O, P 34 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EDO
Query on EDO

A, E, F, H, I, J 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
73W
Query on 73W
G, H, O, P RNA linking C9 H14 N3 O6 P S2 C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.226
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 62.04 α = 90.00
b = 164.07 β = 96.78
c = 176.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-08-18
  • Released Date: 2017-02-08
  • Deposition author(s): Song, H., Ji, X.

Revision History

  • 2017-02-15
    Type: Database references