3BLD

tRNA guanine transglycosylase V233G mutant preQ1 complex structure

Structural Biology Knowledgebase: 3BLD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.151

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3BLD

Classification: TRANSFERASE

Total Structure Weight: 43296.75

Macromolecule Entities
Molecule Chains Length Organism Details
Queuine tRNA-ribosyltransferase A 386 Zymomonas mobilis EC#: 2.4.2.29 IUBMB
Mutation: Y106F, V233G, T312K
Gene Name(s): tgt ZMO0363

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

A 7-DEAZA-7-AMINOMETHYL-GUANINE
C7 H9 N5 O
MEYMBLGOKYDGLZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.151
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.65 α = 90.00
b = 64.88 β = 95.55
c = 70.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-12-11
  • Released Date: 2008-12-16
  • Deposition author(s): Tidten, N., Heine, A., Reuter, K., Klebe, G.

Revision History

  • 2013-07-17
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update