SMTL ID : 5xet.1

Crystal structure of Mycobacterium tuberculosis methionyl-tRNA synthetase bound by methionyl-adenylate (Met-AMP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x ME8: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate(Non-covalent)

ME8.1: 25 residues within 4Å: Chain A: A.17, I.18, A.19, Y.20, H.26, G.28, H.29, Y.31, E.32, D.57, K.62, W.236, A.239, L.240, N.242, Y.243, I.268, G.269, D.271, I.272, H.276, H.298, G.299, F.300, L.301 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.236, A:I.272 Hydrogen bonds: A:Y.20, A:Y.20, A:G.269, A:D.271, A:L.301, A:L.301 Water bridges: A:N.22, A:H.29, A:H.29, A:H.29, A:K.62 Salt bridges: A:H.29 pi-Stacking: A:F.300, A:F.300

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: R.41, N.93, S.95, P.476, E.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.41, A:R.41

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: H.26, V.27, N.303, S.309, V.316 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.309 MG.4: 2 residues within 4Å: Chain A: R.405, H.409 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: Y.31, L.334, L.335, V.338, F.340 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.31, A:L.334, A:V.338 MG.6: 2 residues within 4Å: Chain A: R.336, R.354 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: L.378, Q.450, F.453, R.454 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural characterization of free-state and product-stateMycobacterium tuberculosismethionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism. IUCrJ (2018)

Release Date

2018-07-11

Peptides

Methionine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Methionine--tRNA ligase