SMTL ID : 7ap1.1

Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x RUZ: [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate(Non-covalent)

RUZ.1: 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.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.287 Hydrogen bonds: A:T.237, A:T.237, A:E.239, A:R.268, A:K.289, A:S.358, A:S.391, A:R.397, A:R.397 Water bridges: A:R.283 Salt bridges: A:R.268 pi-Stacking: A:F.287 pi-Cation interactions: A:R.397 RUZ.8: 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.11 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.287 Hydrogen bonds: B:T.237, B:R.268, B:K.289, B:E.355, B:S.358, B:S.391, B:R.397, B:R.397 Water bridges: B:R.283 Salt bridges: B:R.268 pi-Stacking: B:F.287 pi-Cation interactions: B:R.397

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

EDO.2: 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.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: RUZ.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.209 EDO.9: 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.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: RUZ.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.209

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 1 residues within 4Å: Chain A: D.254 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, H2O.1, H2O.3, H2O.4, H2O.5 CA.6: 4 residues within 4Å: Chain A: E.239, S.336, V.362, N.389 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.336 CA.7: 4 residues within 4Å: Chain A: L.328, D.342, E.355, S.358 No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain B: D.254 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.5, H2O.6, H2O.8, H2O.8, H2O.10 CA.13: 4 residues within 4Å: Chain B: E.239, S.336, V.362, N.389 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.336 CA.14: 4 residues within 4Å: Chain B: L.328, D.342, E.355, S.358 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors. Molecules (2020)

Release Date

2020-11-11

Peptides

Serine-tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine-tRNA ligase

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