SMTL ID : 6hi0.1

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-Sulfamoyl)uridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: V.163, M.165, H.173, M.284, Q.286, F.287, D.288, G.396 Chain B: Y.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.288, A:G.396 EDO.2: 6 residues within 4Å: Chain A: N.200, Q.201, D.228, S.229, S.230, N.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.201, A:D.228, A:N.231 Water bridges: A:S.230 EDO.3: 6 residues within 4Å: Chain A: Q.209, P.236, T.237, E.239, R.268 Ligands: FZK.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.209 Water bridges: A:E.270 EDO.8: 9 residues within 4Å: Chain A: Y.194 Chain B: V.163, M.165, H.173, M.284, Q.286, F.287, D.288, G.396 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.288, B:G.396 EDO.9: 6 residues within 4Å: Chain B: N.200, Q.201, D.228, S.229, S.230, N.231 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.201, B:D.228, B:N.231 Water bridges: B:S.230 EDO.10: 6 residues within 4Å: Chain B: Q.209, P.236, T.237, E.239, R.268 Ligands: FZK.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.209 Water bridges: B:E.270, B:E.270

2 x FZK: 5'-O-(N-(L-seryl)-Sulfamoyl)uridine(Non-covalent)

FZK.4: 19 residues within 4Å: Chain A: T.237, E.239, R.268, I.282, R.283, M.284, F.287, K.289, E.291, E.355, I.356, S.357, S.358, N.389, G.390, S.391, A.394, R.397 Ligands: EDO.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.237, A:E.239, A:E.239, A:R.268, A:I.282, A:M.284, A:K.289, A:E.355, A:S.358, A:S.391, A:S.391, A:R.397, A:R.397, A:R.397 Salt bridges: A:R.268 pi-Stacking: A:F.287 pi-Cation interactions: A:R.397 FZK.11: 19 residues within 4Å: Chain B: T.237, E.239, R.268, I.282, R.283, M.284, F.287, K.289, E.291, E.355, I.356, S.357, S.358, N.389, G.390, S.391, A.394, R.397 Ligands: EDO.10 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.239, B:R.268, B:I.282, B:M.284, B:K.289, B:E.355, B:E.355, B:S.358, B:S.391, B:S.391, B:R.397, B:R.397, B:R.397 Salt bridges: B:R.268 pi-Stacking: B:F.287 pi-Cation interactions: B:R.397

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 1 residues within 4Å: Chain A: D.254 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.254, H2O.2, H2O.3 CA.6: 4 residues within 4Å: Chain A: E.239, S.336, V.362, N.389 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain A: L.328, D.342, E.355 No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain B: D.254 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.254, H2O.5, H2O.6 CA.13: 4 residues within 4Å: Chain B: E.239, S.336, V.362, N.389 No protein-ligand interaction detected (PLIP) CA.14: 3 residues within 4Å: Chain B: L.328, D.342, E.355 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, L. et al., Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases. Acs Chem.Biol. (2020)

Release Date

2019-12-18

Peptides

Serine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine--tRNA ligase

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