4YQQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


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:  (by identity cutoff)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43912
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4H7
Query on 4H7

Download Ideal Coordinates CCD File 
B [auth A]6-{[2-(4-methylpiperazin-1-yl)benzyl]amino}pyridine-3-carboxamide
C18 H23 N5 O
BWXGFROIENPTFW-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4H7 BindingDB:  4YQQ IC50: 794 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.39α = 90
b = 94.39β = 90
c = 178.917γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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