4YQN | pdb_00004yqn

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

PDB DOI: https://doi.org/10.2210/pdb4YQN/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.227 (Depositor), 0.224 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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.

Macromolecule Content

Total Structure Weight: 28.64 kDa
Atom Count: 2,026
Modeled Residue Count: 237
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43912
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4H3 Query on 4H3 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-{[(1R,3S,4R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyridine-3-carboxamide C₁₂ H₁₇ N₃ O₃ OOPBXYPWRQVSFZ-BBBLOLIVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
4H3	BindingDB: 4YQN	IC50: 1585 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.227 (Depositor), 0.224 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.684	α = 90
b = 94.684	β = 90
c = 177.761	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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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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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.