SMTL ID : 7osy.1

Human Prolyl-tRNA Synthetase in Complex with L-proline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x PRO: PROLINE(Non-covalent)

PRO.1: 12 residues within 4Å: Chain A: T.121, E.123, R.152, W.169, E.171, H.173, F.216, T.240, H.242, S.272, W.273, G.274 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.169, A:E.171 Hydrogen bonds: A:T.121, A:T.121, A:T.240, A:T.240, A:S.272, P.1 Salt bridges: A:R.152, A:H.242 PRO.6: 12 residues within 4Å: Chain B: T.121, E.123, R.152, W.169, E.171, H.173, F.216, T.240, H.242, S.272, W.273, G.274 13 PLIP interactions: 11 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:W.169, B:E.171 Hydrogen bonds: B:T.121, B:T.121, B:T.121, B:T.240, B:S.272, P.6, P.6 Water bridges: B:R.152, B:R.152 Salt bridges: B:R.152, B:H.242

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.448, C.453, C.495, C.497 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.448, A:C.453, A:C.495, A:C.497 ZN.7: 4 residues within 4Å: Chain B: C.448, C.453, C.495, C.497 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.448, B:C.453, B:C.495, B:C.497

6 x SR: STRONTIUM ION(Non-functional Binders)

SR.3: 3 residues within 4Å: Chain A: E.264, K.265 Ligands: SR.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.264, A:K.265, H2O.2, H2O.3 SR.4: 2 residues within 4Å: Chain A: G.72, E.74 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.72, A:E.74, H2O.2, H2O.3 SR.5: 2 residues within 4Å: Chain A: E.264 Ligands: SR.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.264, A:E.264, H2O.2 SR.8: 4 residues within 4Å: Chain B: E.264, K.265, Q.266 Ligands: SR.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.264, B:K.265, H2O.5, H2O.5 SR.9: 2 residues within 4Å: Chain B: G.72, E.74 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.72 SR.10: 2 residues within 4Å: Chain B: E.264 Ligands: SR.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.264, B:E.264, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, L. et al., Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies. Int J Mol Sci (2021)

Release Date

2021-07-28

Peptides

Bifunctional glutamate/proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional glutamate/proline--tRNA ligase

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