4YQO

Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds

Elkins, P.A.Bonnette, W.G.Williams, S.P.Stuckey, J.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (guanine-N(1)-)-methyltransferase
A
254Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: trmD
EC: 2.1.1.228
Find proteins for P43912 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P43912
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4H1
Query on 4H1

Download SDF File 
Download CCD File 
A
6-({[(1R,3S)-3-(aminomethyl)cyclohexyl]methyl}amino)pyridine-3-carboxamide
C14 H22 N4 O
UUTSJGSKPMLQOF-WDEREUQCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4H1IC50: 501 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 94.389α = 90.00
b = 94.389β = 90.00
c = 178.558γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release