SMTL ID : 7nu3.1

Crystal Structure of Neisseria gonorrhoeae LeuRS E169G mutant in Complex with ATP and L-leucinol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: R.778, P.806, T.807 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.778, A:R.778, A:T.807 Water bridges: A:T.807

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

DCL.2: 9 residues within 4Å: Chain A: F.42, Y.44, D.81, S.511, Y.514, Y.542, H.548, H.552 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:D.81

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

ATP.3: 17 residues within 4Å: Chain A: M.41, Y.44, H.50, G.52, H.53, N.56, G.544, G.545, H.548, Q.581, G.582, M.583, V.584, K.635, M.636, S.637 Ligands: DCL.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.44, A:G.545, A:Q.581, A:V.584, A:V.584, A:K.635, A:S.637, A:S.637 Water bridges: A:K.638 Salt bridges: A:H.53, A:H.548, A:K.635, A:K.635 ATP.5: 10 residues within 4Å: Chain A: Y.256, T.257, T.258, Y.335, V.336, L.337, Y.340, V.345, R.354, R.429 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.258, A:T.258, A:L.337, A:L.337, A:R.354 Water bridges: A:Y.256, A:T.257, A:T.257, A:G.343, A:M.346 Salt bridges: A:K.389, A:R.429, A:R.429

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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