SMTL ID : 6qot.1

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 23 (3-Amino-5-(4-methoxyphenyl)pyrazole)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

2 x 6SD: 3-(4-methoxyphenyl)-1~{H}-pyrazol-5-amine(Non-covalent)

6SD.1: 15 residues within 4Å: Chain A: P.85, T.86, P.87, G.111, R.112, Y.113, G.115, S.134, I.135, G.136, Y.138, V.139, L.140, G.142, G.143 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.87 Hydrogen bonds: A:I.135, A:G.136, A:G.136, A:L.140, A:G.143 6SD.2: 17 residues within 4Å: Chain B: P.85, T.86, P.87, G.111, R.112, Y.113, G.115, S.134, I.135, G.136, Y.138, V.139, L.140, N.141, G.142, G.143 Ligands: EDO.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.87 Hydrogen bonds: B:I.135, B:G.136, B:G.136, B:L.140, B:G.143

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain B: P.85, T.86, P.87, G.115, I.116 Ligands: 6SD.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.86, B:I.116, B:I.116 Water bridges: B:T.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, S.E. et al., Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification. Nucleic Acids Res. (2020)

Release Date

2020-02-26

Peptides

tRNA (guanine-N(1)-)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA (guanine-N(1)-)-methyltransferase

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