4YQ1

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

PDB DOI: https://doi.org/10.2210/pdb4YQ1/pdb

Classification: transferase/transferase inhibitor
Organism(s): Haemophilus influenzae Rd KW20
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

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

Ligand Structure Quality Assessment

This is version 1.1 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.

Macromolecule Content

Total Structure Weight: 28.82 kDa
Atom Count: 2,058
Modelled Residue Count: 244
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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)) Explore P43912 Go to UniProtKB: P43912
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43912
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4FN Query on 4FN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-(1-{[(3-tert-butylbenzoyl)amino]methyl}cyclohexyl)-2,1-benzoxazole-4-carboxamide C₂₆ H₃₁ N₃ O₃ HBQXFVMSOMIMBK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
4FN	BindingDB: 4YQ1	IC50: 5.01 (nM) from 1 assay(s)

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 = 97.466	α = 90
b = 97.466	β = 90
c = 176.697	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Revision History (Full details and data files)

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

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Deposit Data

Help and Resources

4YQ1

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

To Be Published

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)