1P9P

The Crystal Structure of a M1G37 tRNA Methyltransferase, TrmD

Structural Biology Knowledgebase: 1P9P SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1P9P

Classification: TRANSFERASE

Total Structure Weight: 29671.86

Macromolecule Entities
Molecule Chains Length Organism Details
tRNA (Guanine-N(1)-)-methyltransferase A 261 Escherichia coli EC#: 2.1.1.31 IUBMB
Gene Name(s): trmD b2607 JW2588
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SAH
Query on SAH

A S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SAH N/A in BindingDB
Kd: 68 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.196
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.25 α = 90.00
b = 97.25 β = 90.00
c = 62.66 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-12
  • Released Date: 2004-05-18
  • Deposition author(s): Elkins, P.A., Watts, J.M., Zalacain, M., Van Thiel, A., Vitaszka, P.R., Redlak, M., Andraos-Selim, C., Rastinejad, F., Holmes, W.M.

Revision History

  • 2015-08-26
    Type: Source and taxonomy | Details: corrected source organism taxonomy ID
  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values