SMTL ID : 6joe.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

1 x BWR: ~{N}-[[4-[(4-azanylpiperidin-1-yl)methyl]phenyl]methyl]-4-oxidanylidene-3~{H}-thieno[2,3-d]pyrimidine-5-carboxamide(Non-covalent)

BWR.1: 18 residues within 4Å: Chain A: L.111, S.112, P.113, R.138, Y.139, E.140, W.155, S.156, I.157, G.158, Y.160, V.161, L.162, G.164, G.165, P.168 Chain B: D.201, H.204 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.139, A:Y.139, A:Y.139, A:V.161 Hydrogen bonds: A:E.140, A:I.157, A:G.158, A:Y.160, A:L.162, A:L.162 Water bridges: A:G.137 Salt bridges: A:E.140, B:D.201

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: W.241, E.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.241

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

SAM.3: 24 residues within 4Å: Chain A: D.193, S.194, D.201, H.204 Chain B: Y.110, L.111, S.112, P.113, Q.114, G.137, Y.139, E.140, G.141, W.155, S.156, I.157, G.158, Y.160, V.161, L.162, S.163, G.164, G.165, P.168 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.113 Hydrogen bonds: B:Y.110, B:Q.114, B:G.137, B:I.157, B:Y.160, B:L.162, A:S.194, A:D.201, A:D.201, A:D.201 Salt bridges: A:H.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, W. et al., Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism. J.Med.Chem. (2019)

Release Date

2019-09-04

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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