4YQ1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

To Be Published

Elkins, P.A.Bonnette, W.G.Madauss, K.P.Stuckey, J.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (guanine-N(1)-)-methyltransferaseA254Haemophilus influenzae Rd KW20Mutation(s): 0 
Gene Names: trmDHI_0202
EC: 2.1.1.228
UniProt
Find proteins for P43912 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P43912 
Go to UniProtKB:  P43912
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4FN
Query on 4FN

Download Ideal Coordinates CCD File 
B [auth A]N-(1-{[(3-tert-butylbenzoyl)amino]methyl}cyclohexyl)-2,1-benzoxazole-4-carboxamide
C26 H31 N3 O3
HBQXFVMSOMIMBK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4FNIC50:  5.010000228881836   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.466α = 90
b = 97.466β = 90
c = 176.697γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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