1IT8

Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0

Structural Biology Knowledgebase: 1IT8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.232

Literature

Macromolecules
Sequence Display for 1IT8

Classification: TRANSFERASE

Total Structure Weight: 133755.95

Macromolecule Entities
Molecule Chains Length Organism Details
archaeosine tRNA-guanine transglycosylase A, B 582 Pyrococcus horikoshii EC#: 2.4.2.48 IUBMB
Gene Name(s): tgtA PH1116
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PQ0
Query on PQ0

A 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3- D]PYRIMIDINE-5-CARBONITRILE
7-DEAZA-7-CYANO-GUANINE (Synonym)
C7 H5 N5 O
FMKSMYDYKXQYRV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.232
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 100.47 α = 90.00
b = 100.47 β = 90.00
c = 366.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-11
  • Released Date: 2002-05-22
  • Deposition author(s): Ishitani, R., Nureki, O., Fukai, S., Kijimoto, T., Nameki, N., Watanabe, M., Kondo, H., Sekine, M., Okada, N., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

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