SMTL ID : 7nuc.1

Crystal Structure of Neisseria gonorrhoeae LeuRS L550G mutant in Complex with ATP and L-leucinol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: R.778, P.806, T.807 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.778, A:R.778, A:A.803, A:T.807, A:T.807 EDO.5: 4 residues within 4Å: Chain A: P.464, V.465, V.466, R.500 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.466, A:V.466

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 25 residues within 4Å: Chain A: M.41, P.43, Y.44, S.46, H.50, G.52, H.53, N.56, Y.57, R.179, G.544, G.545, E.547, H.548, Q.581, G.582, M.583, V.584, K.635, M.636, S.637, K.638, S.639 Ligands: MG.3, DCL.4 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:Y.44, A:S.46, A:G.545, A:E.547, A:Q.581, A:V.584, A:K.635, A:M.636, A:M.636, A:K.638, A:S.639, A:S.639 Water bridges: A:R.179, A:E.547, A:E.547, A:E.547, A:E.547 Salt bridges: A:H.50, A:H.53, A:H.53, A:R.179, A:K.635, A:K.635, A:K.638, A:K.638, A:K.638

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 2 residues within 4Å: Ligands: ATP.2, DCL.4 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: K.209 No protein-ligand interaction detected (PLIP)

1 x DCL: 2-AMINO-4-METHYL-PENTAN-1-OL(Non-covalent)

DCL.4: 13 residues within 4Å: Chain A: M.41, F.42, P.43, Y.44, D.81, F.508, S.511, Y.514, Y.542, H.548, H.552 Ligands: ATP.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.42, A:F.508, A:H.552 Hydrogen bonds: A:D.81, A:D.81 Water bridges: A:H.548

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.450, C.453, C.491, C.494 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.450, A:C.453, A:C.491, A:C.494

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, L. et al., Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip. Commun Biol (2022)

Release Date

2022-08-31

Peptides

Leucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine--tRNA ligase

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