SMTL ID : 7f97.2 (1 other biounit)

Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L97

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 x PRO: PROLINE(Non-covalent)

PRO.1: 13 residues within 4Å: Chain A: T.110, E.112, R.141, W.158, E.160, H.162, F.205, T.229, H.231, S.259, W.260, G.261 Ligands: 1XK.2 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.158, A:E.160 Hydrogen bonds: A:T.110, A:T.110, A:T.229, A:T.229, A:S.259, P.1 Salt bridges: A:R.141, A:H.231 PRO.6: 12 residues within 4Å: Chain B: T.110, E.112, R.141, W.158, E.160, F.205, T.229, H.231, S.259, W.260, G.261 Ligands: 1XK.7 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.158, B:E.160 Hydrogen bonds: B:T.110, B:T.110, B:T.229, B:T.229, B:S.259, P.6 Water bridges: B:R.141, B:R.141 Salt bridges: B:R.141, B:H.231

2 x 1XK: 4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide(Non-covalent)

1XK.2: 21 residues within 4Å: Chain A: R.141, E.143, K.145, Q.146, P.147, F.150, I.151, R.152, T.153, R.154, F.156, W.158, Q.226, A.227, A.228, T.229, G.261, T.263, R.265, Y.497 Ligands: PRO.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.143, A:E.143, A:K.145, A:R.152, A:R.154, A:F.156, A:W.158, A:T.263 Hydrogen bonds: A:E.143, A:R.152, A:T.153, A:T.153, A:A.228, A:T.263 Water bridges: A:T.263, A:T.263 pi-Stacking: A:F.156 1XK.7: 22 residues within 4Å: Chain B: R.141, E.143, K.145, Q.146, P.147, F.150, I.151, R.152, T.153, R.154, F.156, W.158, Q.226, A.227, A.228, T.229, G.261, C.262, T.263, R.265, Y.497 Ligands: PRO.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.143, B:R.152, B:F.156, B:W.158, B:T.263 Hydrogen bonds: B:E.143, B:R.152, B:T.153, B:T.153, B:Q.226, B:Q.226, B:T.263 pi-Stacking: B:F.156

1 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.3: 5 residues within 4Å: Chain A: K.121, W.122, D.128 Chain B: E.25, R.39 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.121, A:K.121, A:D.128, B:R.39

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, S. et al., Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L97. To Be Published

Release Date

2023-01-04

Peptides

Proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Proline--tRNA ligase

Related Entries With Identical Sequence