SMTL ID : 5zhj.1

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with S-adenosyl homocysteine (SAH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 18 residues within 4Å: Chain A: P.83, T.84, P.85, G.109, Y.111, E.112, G.113, V.131, S.132, I.133, G.134, Y.136, V.137, L.138, P.139, G.140, G.141, A.144 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.85 Hydrogen bonds: A:P.83, A:G.109, A:E.112, A:I.133, A:Y.136, A:L.138 Water bridges: A:T.84 SAH.3: 18 residues within 4Å: Chain B: P.83, T.84, P.85, G.109, Y.111, E.112, G.113, V.131, S.132, I.133, G.134, Y.136, V.137, L.138, P.139, G.140, G.141, A.144 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.85 Hydrogen bonds: B:P.83, B:T.84, B:G.109, B:E.112, B:I.133, B:Y.136, B:L.138 Water bridges: B:T.84

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: P.10, V.34, H.35, D.36, R.39 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.36, A:R.39 Water bridges: A:D.36 GOL.4: 5 residues within 4Å: Chain B: P.10, V.34, H.35, D.36, R.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.36, B:R.39

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

2019-03-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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

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