SMTL ID : 7v9d.1

Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with inhibitor L95 and azetidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x JE6: ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide(Non-covalent)

JE6.1: 20 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 Ligands: 02A.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.141, A:E.143, A:E.143, A:K.145, A:P.147, A:R.154, A:F.156, A:W.158, A:W.158, A:T.229, A:T.263 Hydrogen bonds: A:R.152, A:T.153, A:T.153 pi-Stacking: A:F.156 JE6.8: 20 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, T.263, R.265 Ligands: 02A.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:R.141, B:E.143, B:E.143, B:K.145, B:P.147, B:R.154, B:F.156, B:W.158, B:W.158, B:T.229, B:T.263 Hydrogen bonds: B:R.152, B:T.153, B:T.153, B:T.263 Water bridges: B:E.143 pi-Stacking: B:F.156

2 x 02A: (2S)-azetidine-2-carboxylic acid(Non-covalent)

02A.2: 13 residues within 4Å: Chain A: T.110, E.112, R.141, W.158, E.160, F.205, T.229, H.231, S.259, W.260, G.261 Ligands: JE6.1, ACT.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.110, A:S.259 Water bridges: A:R.141, A:R.141 Salt bridges: A:R.141, A:H.231 02A.9: 13 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: JE6.8, ACT.13 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.110, B:T.110, B:S.259 Water bridges: B:R.141, B:R.141 Salt bridges: B:R.141, B:H.231

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

EDO.3: 4 residues within 4Å: Chain A: Y.44, E.47, C.48, A.51 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: I.198, P.468, L.469, Q.471, R.489 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.489 EDO.5: 1 residues within 4Å: Chain A: R.446 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain B: Y.44, E.47, C.48, A.51 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain B: I.198, P.468, L.469, Q.471, R.489 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.489 EDO.12: 1 residues within 4Å: Chain B: R.446 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 7 residues within 4Å: Chain A: E.203, K.204, F.205, Q.226, T.229, H.231 Ligands: 02A.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.226, A:T.229, A:T.229 Salt bridges: A:H.231 ACT.13: 7 residues within 4Å: Chain B: E.203, K.204, F.205, Q.226, T.229, H.231 Ligands: 02A.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.226, B:T.229 Salt bridges: B:H.231

2 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.7: 4 residues within 4Å: Chain A: F.176, I.198, F.210, R.489 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.198, A:F.210 Hydrogen bonds: A:R.489, A:R.489 BU1.14: 4 residues within 4Å: Chain B: F.176, I.198, F.210, R.489 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.198, B:F.210 Hydrogen bonds: B:R.489, B:R.489

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manickam, Y. et al., Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with inhibitor L95 and azetidine. To Be Published

Release Date

2022-09-07

Peptides

Proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Proline--tRNA ligase

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