SMTL ID : 6spn.1

Structure of the Escherichia coli methionyl-tRNA synthetase complexed with beta-methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: C.166, K.168, C.169, S.171, C.179, V.181, C.182, A.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.166, A:C.169, A:C.179, A:C.182

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 2 residues within 4Å: Chain A: Q.84, K.153 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.153 Water bridges: A:Q.84, A:Q.84, A:Q.84 Salt bridges: A:K.153, A:K.153

2 x B3M: (3R)-3-amino-5-(methylsulfanyl)pentanoic acid(Non-covalent)

B3M.3: 11 residues within 4Å: Chain A: A.33, L.34, P.35, Y.36, D.73, W.274, A.277, P.278, Y.281, I.318, H.322 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.274 Hydrogen bonds: A:D.73, A:D.73 B3M.4: 10 residues within 4Å: Chain A: Q.234, V.235, K.238, W.242, K.316, D.317, V.319, V.343, Y.346, I.388 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.238 Hydrogen bonds: A:Y.346

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: A.434, Q.479, V.484, R.490, D.493, A.496, I.497 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.490 Water bridges: A:Q.479, A:A.492, A:D.493

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nigro, G. et al., Use of beta3-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase. J.Struct.Biol. (2020)

Release Date

2020-01-01

Peptides

Methionine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine--tRNA ligase

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