SMTL ID : 6s30.1

Crystal Structure of Seryl-tRNA Synthetase from Klebsiella pneumoniae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

4 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.288, 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.6: 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.288, B:D.288, B:G.396 EDO.7: 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

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: L.328, D.332, D.342 No protein-ligand interaction detected (PLIP) CA.4: 1 residues within 4Å: Chain A: N.389 No protein-ligand interaction detected (PLIP) 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.8: 3 residues within 4Å: Chain B: L.328, D.332, D.342 No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain B: N.389 No protein-ligand interaction detected (PLIP) CA.10: 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.7

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

2020-01-08

Peptides

Serine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine--tRNA ligase

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