SMTL ID : 6hhz.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.201, A:D.228, A:N.231, A:N.231 Water bridges: A:D.202, A:S.230 EDO.3: 6 residues within 4Å: Chain A: Q.209, P.236, T.237, E.239, R.268 Ligands: FZQ.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.209 EDO.10: 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.11: 6 residues within 4Å: Chain B: N.200, Q.201, D.228, S.229, S.230, N.231 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.201, B:D.228, B:N.231, B:N.231 Water bridges: B:D.202, B:S.230 EDO.12: 6 residues within 4Å: Chain B: Q.209, P.236, T.237, E.239, R.268 Ligands: FZQ.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.209

2 x FZQ: 5'-O-(N-(L-seryl)-sulfamoyl)cytidine(Non-covalent)

FZQ.4: 20 residues within 4Å: Chain A: T.237, E.239, R.268, E.270, 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:E.270, A:M.284, A:K.289, A:E.355, A:S.358, A:S.391, A:R.397, A:R.397, A:R.397 Water bridges: A:S.358 Salt bridges: A:R.268 pi-Stacking: A:F.287 pi-Cation interactions: A:R.397 FZQ.13: 20 residues within 4Å: Chain B: T.237, E.239, R.268, E.270, 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.12 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.239, B:R.268, B:E.270, B:M.284, B:K.289, B:E.355, B:E.355, B:S.358, B:S.391, B:R.397, B:R.397, B:R.397 Water bridges: B:S.358 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 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.254, H2O.2, H2O.3, H2O.7 CA.6: 4 residues within 4Å: Chain A: L.328, D.342, E.355, S.358 No protein-ligand interaction detected (PLIP) CA.7: 4 residues within 4Å: Chain A: E.239, S.336, V.362, N.389 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain B: D.254 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.254, H2O.9, H2O.10, H2O.14 CA.15: 4 residues within 4Å: Chain B: L.328, D.342, E.355, S.358 No protein-ligand interaction detected (PLIP) CA.16: 4 residues within 4Å: Chain B: E.239, S.336, V.362, N.389 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Chain A: R.8 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: R.8 Ligand excluded by PLIP

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 4 residues within 4Å: Chain A: M.1, L.7, I.96, A.100 No protein-ligand interaction detected (PLIP) 1PE.18: 4 residues within 4Å: Chain B: M.1, L.7, I.96, A.100 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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