SMTL ID : 7yp8.1

Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Leucyl-sulfamoyl 3-deazaadenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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, A:T.807

1 x JIE: [(2R,3S,4R,5R)-5-(4-azanylimidazo[4,5-c]pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-[(2S)-2-azanyl-4-methyl-pentanoyl]sulfamate(Non-covalent)

JIE.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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:M.41, A:F.42, A:Q.581 Hydrogen bonds: A:F.42, A:Y.44, A:D.81, A:G.545, A:Q.581, A:V.584, A:V.584, A:M.636 Water bridges: A:K.635 Salt bridges: A:H.53

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 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., The essential role of a structured water in base recognition of Class II aminoacyl-tRNA synthetases. To be published

Release Date

2024-02-07

Peptides

Leucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine--tRNA ligase

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