SMTL ID : 6afk.1

Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 25 residues within 4Å: Chain A: Y.110, L.111, S.112, P.113, Q.114, G.137, R.138, Y.139, E.140, G.141, S.156, I.157, G.158, Y.160, V.161, L.162, S.163, G.164, G.165, P.168 Chain B: D.188, D.193, S.194, D.201, H.204 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.114, A:Q.114, A:G.137, A:I.157, A:G.158, A:Y.160, A:L.162, B:S.194, B:D.201, B:D.201 Water bridges: A:Y.110 Salt bridges: B:D.188

1 x 9WO: N-{(3S)-1-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]piperidin-3-yl}-1H-indole-2-carboxamide(Non-covalent)

9WO.2: 19 residues within 4Å: Chain A: R.178 Chain B: Y.110, L.111, S.112, P.113, G.137, Y.139, E.140, G.141, S.156, I.157, G.158, Y.160, V.161, L.162, S.163, G.164, G.165, P.168 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.168 Hydrogen bonds: B:Y.139, B:I.157, B:G.158, B:L.162, B:L.162 Water bridges: B:E.140, A:D.201 pi-Cation interactions: A:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, W. et al., Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N1G37) Methyltransferase (TrmD) Inhibitors. Acs Infect Dis. (2019)

Release Date

2019-08-14

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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