SMTL ID : 6qr8.1

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x JDH: 5-azanyl-3-[1-[[4-[(4-methylpiperazin-1-yl)methyl]phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile(Non-covalent)

JDH.1: 19 residues within 4Å: Chain A: P.85, T.86, P.87, G.111, R.112, Y.113, E.114, V.133, S.134, I.135, G.136, Y.138, V.139, L.140, N.141, G.142, G.143, A.146 Chain B: L.180 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.87, A:V.139 Hydrogen bonds: A:T.86, A:I.135, A:G.136, A:G.136, A:Y.138, A:L.140 JDH.2: 20 residues within 4Å: Chain A: E.182 Chain B: P.85, T.86, P.87, G.111, R.112, Y.113, E.114, G.115, V.133, S.134, I.135, G.136, Y.138, V.139, L.140, N.141, G.142, G.143, A.146 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.87, B:V.139 Hydrogen bonds: B:T.86, B:I.135, B:G.136, B:G.136, B:Y.138, B:L.140 Salt bridges: B:E.114

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

2020-03-18

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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