SMTL ID : 6t7k.1

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with NCP-26 and L-Proline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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: MU5.2 12 PLIP interactions: 2 Ligand-Ligand interactions, 10 interactions with chain A Hydrogen bonds: P.1, P.1, A:T.117, A:T.117, A:T.117, A:S.266 Hydrophobic interactions: A:W.165, A:E.167 Water bridges: A:R.148, A:R.148 Salt bridges: A:R.148, A:H.238

1 x MU5: ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide(Non-covalent)

MU5.2: 19 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, Q.233, T.236, G.268, T.270, R.272 Ligands: PRO.1, EDO.18 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.148, A:E.150, A:E.150, A:K.152, A:R.159, A:W.165, A:T.236 Hydrogen bonds: A:T.160, A:T.160, A:T.270, A:R.272 pi-Stacking: A:F.163

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

EDO.3: 4 residues within 4Å: Chain A: S.21, Y.24, M.279, Y.504 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: Y.51, E.54, C.55 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: K.16, E.227, T.280, H.281, G.282, K.409 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: A.48, L.289, S.294, K.295, Y.296, I.353 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: E.63, K.66, R.191 Ligands: EDO.17, EDO.22 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: N.61, K.65, V.69, E.70, N.71 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: K.206, E.210, T.218, Q.233, T.236, H.238 Ligands: EDO.18 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: I.205, P.475, L.476, Q.478, R.496 Ligands: EDO.11 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: F.183, I.205, F.217 Ligands: EDO.10 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: R.190, K.203 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: P.95 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: K.285, E.349, R.356, V.372, R.373, R.374, N.377 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: T.242, Q.260, Y.261, H.263 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: V.179, K.180, F.183 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: K.62, E.63, K.66, R.191 Ligands: EDO.7 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: Q.233, R.272, Y.504 Ligands: MU5.2, EDO.9 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: R.336, A.337, S.338 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: V.29, K.30 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: Y.36, Y.37, D.38 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: L.67, D.184, D.187, L.188 Ligands: EDO.7 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: Y.133, L.136, P.137, K.173, E.177 Ligand excluded by PLIP

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 NCP-26 and L-Proline. To Be Published

Release Date

2020-11-18

Peptides

Proline--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Proline--tRNA ligase

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