SMTL ID : 5v58.1

Crystal structure of human prolyl-tRNA synthetase in complex with Aze-SA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-dimer

Ligands

2 x 8X1: 5'-O-{[(2S)-azetidine-2-carbonyl]sulfamoyl}adenosine(Non-covalent)

8X1.1: 21 residues within 4Å: Chain A: T.128, E.130, R.159, E.161, F.168, L.169, R.170, T.171, F.174, W.176, E.178, H.180, F.223, Q.244, G.246, T.247, H.249, W.280, G.281, T.283, R.285 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.176 Hydrogen bonds: A:T.128, A:R.159, A:R.159, A:E.161, A:T.171, A:Q.244, A:Q.244, A:T.247, A:T.247, A:T.247, A:H.249, A:S.279, A:R.285 Salt bridges: A:R.159, A:H.249 pi-Stacking: A:F.174 pi-Cation interactions: A:R.285 8X1.3: 21 residues within 4Å: Chain B: T.128, E.130, R.159, E.161, F.168, L.169, R.170, T.171, F.174, W.176, E.178, H.180, F.223, Q.244, G.246, T.247, H.249, W.280, G.281, T.283, R.285 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.176 Hydrogen bonds: B:T.128, B:T.128, B:R.159, B:R.159, B:E.161, B:T.171, B:Q.244, B:Q.244, B:T.247, B:T.247, B:T.247, B:H.249, B:S.279, B:T.283, B:R.285 Salt bridges: B:R.159, B:H.249 pi-Stacking: B:F.174 pi-Cation interactions: B:R.285

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.455, C.460, C.502, C.504, N.507 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.455, A:C.502 ZN.4: 5 residues within 4Å: Chain B: C.455, C.460, C.502, C.504, N.507 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.455, B:C.502

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, Y. et al., Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid. Nat Commun (2017)

Release Date

2018-01-10

Peptides

Bifunctional glutamate/proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bifunctional glutamate/proline--tRNA ligase

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