SMTL ID : 6r1m.1

Crystal structure of E. coli seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

SSA.1: 20 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 17 PLIP interactions: 17 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:E.355, A:S.358, A:S.391, A:R.397 Water bridges: A:R.268, A:S.358 Salt bridges: A:R.268 pi-Stacking: A:F.287, A:F.287 SSA.12: 20 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 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.358, B:S.358, B:S.391, B:R.397 Water bridges: B:R.268, B:R.268, B:R.283, B:R.283 Salt bridges: B:R.268 pi-Stacking: B:F.287, B:F.287

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: R.283, R.354, E.355, R.397 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.354, A:E.355, A:E.355 Salt bridges: A:R.283, A:R.354, A:R.397 PO4.13: 6 residues within 4Å: Chain B: R.276, D.277, R.283, R.354, E.355, R.397 9 PLIP interactions: 9 interactions with chain B Water bridges: B:R.283, B:R.354, B:E.355, B:E.355, B:R.397 Salt bridges: B:R.276, B:R.283, B:R.354, B:R.397 PO4.14: 3 residues within 4Å: Chain B: N.120, V.121, E.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.120, B:E.122 PO4.15: 3 residues within 4Å: Chain B: V.140, T.141, R.279 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.279

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

EDO.3: 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 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: L.181, E.192, N.193, A.262, H.263 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: N.200, Q.201, D.228, T.229, S.230, N.231 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: G.167, Q.168, R.171, R.174 Chain B: T.185, E.192 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: R.130, G.320, P.322, N.405, Y.406 Ligands: EDO.10 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: A.152, A.153, K.156 Chain B: R.247, E.249 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: K.166 Chain B: L.245, V.246, E.249, I.258, M.260 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: W.126, G.127, T.128, G.320, P.322 Ligands: EDO.7 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: P.421, Y.422 Chain B: P.421, Y.422 Ligand excluded by PLIP EDO.16: 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 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: N.200, Q.201, D.228, T.229, S.230, N.231 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: L.181, E.192, N.193, A.262, H.263 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: R.130, G.320, P.322, N.405, Y.406 Ligands: EDO.20 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: W.126, G.127, T.128, G.320, P.322 Ligands: EDO.19 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: F.179, D.182, L.183, E.186, Q.187, Y.422 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: N.105, L.106, P.107, A.108, C.338, W.363 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: L.6, A.13, K.17, L.106 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cain, R. et al., Structure-Guided Enhancement of Selectivity of Chemical Probe Inhibitors Targeting Bacterial Seryl-tRNA Synthetase. J.Med.Chem. (2019)

Release Date

2020-01-22

Peptides

Serine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Serine--tRNA ligase

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