SMTL ID : 7qb7.1

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT345 and L-Proline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x PRO: PROLINE(Non-covalent)

PRO.1: 13 residues within 4Å: Chain A: T.117, E.119, R.148, W.165, E.167, H.169, F.212, T.236, H.238, S.266, W.267, G.268 Ligands: 9X2.15 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:W.165, A:E.167 Hydrogen bonds: A:T.117, A:T.117, A:T.117, A:S.266, P.1, P.1 Water bridges: A:R.148, A:R.148 Salt bridges: A:R.148, A:H.238

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

EDO.2: 6 residues within 4Å: Chain A: I.205, P.475, L.476, Q.478, R.496 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.496 EDO.3: 6 residues within 4Å: Chain A: A.48, L.289, S.294, K.295, Y.296, I.353 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.295, A:Y.296 Water bridges: A:P.47, A:A.48 EDO.4: 5 residues within 4Å: Chain A: N.61, K.65, V.69, E.70, N.71 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.71, A:N.71 Water bridges: A:N.61, A:N.71, A:N.71 EDO.5: 5 residues within 4Å: Chain A: Y.133, L.136, P.137, K.173, E.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.136, A:E.177 EDO.6: 2 residues within 4Å: Chain A: Y.51, E.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.54 EDO.7: 3 residues within 4Å: Chain A: I.205, F.217 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.496 EDO.8: 1 residues within 4Å: Chain A: F.183 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: K.128, R.131, D.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.131 EDO.10: 4 residues within 4Å: Chain A: E.251, K.259, Q.260, Y.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.251 EDO.11: 2 residues within 4Å: Chain A: Y.37, D.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.38 Water bridges: A:Y.37, A:S.40 EDO.12: 7 residues within 4Å: Chain A: C.42, Y.43, T.160, E.162, F.163, L.164, T.271 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.43, A:Y.43, A:T.160, A:L.164, A:T.271, A:T.271 EDO.13: 5 residues within 4Å: Chain A: V.332, Y.333, D.334, R.336, W.348 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.335 EDO.14: 3 residues within 4Å: Chain A: E.195, N.292, H.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.292, A:H.399

1 x 9X2: ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-[[4-[[[(2~{S})-pyrrolidin-2-yl]carbonylamino]methyl]piperidin-1-yl]carbonylamino]pyrazine-2-carboxamide(Non-covalent)

9X2.15: 24 residues within 4Å: Chain A: R.148, E.150, K.152, Q.153, P.154, F.157, I.158, R.159, T.160, R.161, F.163, W.165, K.206, E.210, K.211, F.212, T.218, Q.233, A.235, T.236, H.238, T.270, R.272 Ligands: PRO.1 17 PLIP interactions: 16 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:R.148, A:E.150, A:E.150, A:K.152, A:R.159, A:R.161, A:T.236 Hydrogen bonds: A:T.160, A:T.160, A:Q.233, A:T.270, A:R.272, A:R.272, P.1 Water bridges: A:R.148, A:R.148 pi-Stacking: A:F.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT345. To Be Published

Release Date

2021-12-08

Peptides

Proline--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Proline--tRNA ligase

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