4ISZ

RNA ligase RtcB in complex with GTP alphaS and Mn(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.165

Literature

Macromolecules
Sequence Display for 4ISZ

Classification: LIGASE

Total Structure Weight: 111219.10

Macromolecule Entities
Molecule Chains Length Organism Details
tRNA-splicing ligase RtcB A, B 481 Pyrococcus horikoshii EC#: 6.5.1 IUBMB
Gene Name(s): rtcB PH1602
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE
C10 H16 N5 O13 P3 S
YRUWXBKVSXSSGS-KIOICMOXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

A, B SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.165
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 81.11 α = 90.00
b = 138.91 β = 90.00
c = 149.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-17
  • Released Date: 2013-04-10
  • Deposition author(s): Desai, K.K., Bingman, C.A., Phillips Jr., G.N., Raines, R.T.

Revision History

  • Version 1_0: 2013-04-10

    Type: Initial release

  • Version 1_1: 2013-05-01

    Type: Database references

  • Version 1_2: 2017-08-09

    Type: Source and taxonomy