1Q2S

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

Structural Biology Knowledgebase: 1Q2S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Q2S

Classification: Transferase / RNA

Total Structure Weight: 184838.89


Macromolecule Entities
Molecule Chains Length Organism Details
Queuine tRNA-ribosyltransferase A, B, C, D 386 Zymomonas mobilis EC#: 2.4.2.29 IUBMB
Gene Name(s): tgt ZMO0363
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(PQ1)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3' E 20 synthetic
RNA (5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(N)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3') F 20 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
9DG
Query on 9DG

C 9-DEAZAGUANINE
C6 H6 N4 O
FFYPRJYSJODFFD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
PQ1
Query on PQ1
E RNA LINKING C12 H18 N5 O8 P --
N
Query on N
F RNA LINKING C5 H11 O7 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.180
  • Space Group: I 4
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 261.96 α = 90.00
b = 261.96 β = 90.00
c = 55.55 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-07-25
  • Released Date: 2003-09-09
  • Deposition author(s): Xie, W., Liu, X., Huang, R.H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4