SMTL ID : 7nu8.1

Crystal Structure of Neisseria gonorrhoeae LeuRS in Complex with the Reaction Intermediate Leu-AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: R.778, A.803, P.806, T.807 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.778, A:R.778, A:T.807, A:T.807

1 x USB: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate(Non-covalent)

USB.2: 24 residues within 4Å: Chain A: M.41, F.42, P.43, Y.44, H.50, G.52, H.53, N.56, Y.57, D.81, S.511, Y.514, Y.542, G.544, G.545, E.547, H.548, H.552, Q.581, G.582, M.583, V.584, K.635, M.636 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:Y.44, A:D.81, A:G.545, A:E.547, A:Q.581, A:V.584, A:V.584, A:M.636 Salt bridges: A:H.53, A:H.548

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

ATP.3: 11 residues within 4Å: Chain A: S.228, Y.256, T.257, T.258, Y.335, V.336, L.337, Y.340, V.345, R.354, R.429 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.228, A:T.258, A:T.258, A:L.337, A:L.337, A:R.354 Water bridges: A:Y.256, A:T.257, A:D.342, A:G.343, A:M.346, A:R.429 Salt bridges: 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.5: 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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