SMTL ID : 7ndm.1

Crystal structure of the heterocyclic toxin methyltransferase from Mycobacterium tuberculosis with bound substrate 4-hydroxyisoquinolin-1(2H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

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

SAH.1: 17 residues within 4Å: Chain A: F.29, Y.33, W.48, G.74, C.75, G.76, D.95, L.96, S.97, A.121, D.122, A.123, S.139, T.140, L.141, S.144 Ligands: NA.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.33, A:Y.33, A:G.76, A:L.96, A:D.122, A:D.122, A:A.123, A:S.139 Water bridges: A:Y.33, A:W.48, A:S.124, A:S.139

1 x U8N: 4-oxidanyl-2~{H}-isoquinolin-1-one(Non-covalent)

U8N.2: 7 residues within 4Å: Chain A: P.47, W.48, F.172, I.182, A.210, F.212, F.216 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.47, A:W.48, A:W.48, A:F.172, A:A.210, A:F.212 Water bridges: A:S.144

3 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: S.144, M.145 Ligands: SAH.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.144 NA.4: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.56, A:E.56 NA.5: 3 residues within 4Å: Chain A: I.61, R.87, H.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.87, A:H.89

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.6: 3 residues within 4Å: Chain A: R.105, E.119, V.120 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.119, A:E.119, A:V.120 Salt bridges: A:R.105, A:R.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sartor, P. et al., Structural basis of O-methylation of (2-heptyl-)1-hydroxyquinolin-4(1H)-one and related compounds by the heterocyclic toxin methyltransferase Rv0560c of Mycobacterium tuberculosis. J.Struct.Biol. (2021)

Release Date

2021-09-22

Peptides

Heterocyclic toxin methyltransferase (Rv0560c): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heterocyclic toxin methyltransferase (Rv0560c)

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