3ZGZ

Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation

Structural Biology Knowledgebase: 3ZGZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.187

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZGZ

Classification: LIGASE / RNA

Total Structure Weight: 257049.31


Macromolecule Entities
Molecule Chains Length Organism Details
LEUCINE--TRNA LIGASE A, D 880 Escherichia coli EC#: 6.1.1.4 IUBMB
Gene Name(s): leuS b0642 JW0637
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
TRNA-LEU UAA ISOACCEPTOR B, E 88 Escherichia coli

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
84T
Query on 84T

A, D [(2S,4S,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl- oxolan-2-yl]methoxy-N-[(2S,3R)-4-methyl-2,3- bis(oxidanyl)pentanoyl]phosphonamidic acid
C16 H25 N6 O8 P
KHSKVNAFZAVNFC-UVIICUSPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B, E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.187
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 158.58 α = 90.00
b = 68.19 β = 105.53
c = 226.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-19
  • Released Date: 2013-01-30
  • Deposition author(s): Chopra, S., Palencia, A., Virus, C., Tripathy, A., Temple, B.R., Velazquez-Campoy, A., Cusack, S., Reader, J.S.

Revision History

  • 2013-02-13
    Type: Citation | Details: JRNL