4YPZ

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

• PDB DOI: https://doi.org/10.2210/pdb4YPZ/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Haemophilus influenzae Rd KW20
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-13 Released: 2016-03-16 
• Deposition Author(s): Elkins, P.A., Bonnette, W.G., Stuckey, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.194 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.53 kDa 
• Atom Count: 2,037 
• Modelled Residue Count: 236 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A	254	Haemophilus influenzae Rd KW20	Mutation(s): 0  Gene Names: trmD, HI_0202 EC: 2.1.1.228
UniProt
Find proteins for P43912 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Go to UniProtKB:  P43912

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4FL	B [auth A]	4-(1H-imidazol-2-yl)pyridine C8 H7 N3 QWZSAEUNIBEKIZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4FL	BindingDB:  4YPZ	IC50: 3.16e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.194 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.773	α = 90
b = 93.773	β = 90
c = 179.162	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Elkins, P.A., Bonnette, W.G., Stuckey, J.A.

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description