SMTL ID : 6spq.1

Structure of the Escherichia coli methionyl-tRNA synthetase variant VI298 complexed with methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 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 MET: METHIONINE(Non-covalent)

MET.2: 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 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.274 Hydrogen bonds: A:L.34, A:L.34, A:D.73, M.2 Water bridges: A:Y.36, A:H.45

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

CIT.3: 2 residues within 4Å: Chain A: Q.84, K.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.153 Water bridges: A:Q.84, A:Q.84 Salt bridges: A:K.153, A:K.153 CIT.4: 8 residues within 4Å: Chain A: T.77, P.78, P.158, R.160, F.161, R.254, Y.258, Y.272 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.158 Hydrogen bonds: A:T.77, A:Y.272 Water bridges: A:D.159, A:D.159, A:R.160, A:R.254, A:R.254, A:Y.258, A:W.274 Salt bridges: A:R.160, A:R.254, A:R.254

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: A.434, Q.479, V.484, R.490, D.493, A.496, I.497 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.479, A:Q.479, A:R.490 GOL.6: 7 residues within 4Å: Chain A: E.478, Q.479, A.480, V.483, V.484, R.490 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.490, A:R.490 GOL.7: 7 residues within 4Å: Chain A: W.55, Y.311, N.340, F.342, E.454, S.455, R.456 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.340 Water bridges: A:W.55, A:A.230, A:S.339, A:E.454, A:R.456 GOL.8: 5 residues within 4Å: Chain A: H.119, S.120, E.121, R.124, F.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.121, A:R.124, A:R.124 Water bridges: A:H.119

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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