SMTL ID : 6h9x.1

Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x SSA: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE(Non-covalent)

SSA.1: 22 residues within 4Å: Chain A: T.237, E.239, R.268, E.270, L.281, 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.4, CA.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.237, A:T.237, A:E.239, A:R.268, A:E.270, A:M.284, A:K.289, A:E.355, A:S.357, A:S.358, A:S.358, A:S.391, A:R.397, A:R.397 pi-Stacking: A:F.287, A:F.287 Salt bridges: A:R.268 pi-Cation interactions: A:R.397 Water bridges: A:R.268 SSA.8: 22 residues within 4Å: Chain B: T.237, E.239, R.268, E.270, L.281, 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.11, CA.12 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.237, B:R.268, B:E.270, B:M.284, B:K.289, B:E.355, B:E.355, B:S.357, B:S.358, B:S.358, B:S.391, B:R.397, B:R.397 pi-Stacking: B:F.287, B:F.287 Salt bridges: B:R.268 pi-Cation interactions: B:R.397 Water bridges: B:R.268

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

EDO.2: 8 residues within 4Å: Chain A: M.165, H.173, M.284, Q.286, F.287, D.288, G.396 Chain B: Y.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.288, A:D.288, A:G.396 EDO.3: 6 residues within 4Å: Chain A: N.200, Q.201, D.228, S.229, S.230, N.231 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.201, A:D.228, A:N.231 Water bridges: A:D.202, A:S.230 EDO.4: 5 residues within 4Å: Chain A: Q.209, T.237, E.239, R.268 Ligands: SSA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.209 EDO.9: 8 residues within 4Å: Chain A: Y.194 Chain B: M.165, H.173, M.284, Q.286, F.287, D.288, G.396 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.288, B:D.288, B:G.396 EDO.10: 6 residues within 4Å: Chain B: N.200, Q.201, D.228, S.229, S.230, N.231 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.201, B:D.228, B:N.231 Water bridges: B:D.202, B:S.230 EDO.11: 5 residues within 4Å: Chain B: Q.209, T.237, E.239, R.268 Ligands: SSA.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.209

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.342, E.355, S.358 Ligands: SSA.1 No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain A: E.239, S.336, V.362, N.389 No protein-ligand interaction detected (PLIP) CA.7: 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.5, H2O.8 CA.12: 4 residues within 4Å: Chain B: D.342, E.355, S.358 Ligands: SSA.8 No protein-ligand interaction detected (PLIP) CA.13: 4 residues within 4Å: Chain B: E.239, S.336, V.362, N.389 No protein-ligand interaction detected (PLIP) CA.14: 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.12, H2O.15

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

De Ruysscher, D. et al., Acylated sulfonamide adenosines as potent inhibitors of the adenylate-forming enzyme superfamily. Eur.J.Med.Chem. (2019)

Release Date

2019-05-15

Peptides

Serine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine--tRNA ligase

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