SMTL ID : 6uyh.1

Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with halofuginone and AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 16 residues within 4Å: Chain A: R.150, E.152, F.159, I.160, R.161, S.162, F.165, W.167, Q.235, G.236, G.237, T.238, S.272, R.274 Ligands: HFG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.150, A:E.152, A:R.161, A:R.161, A:S.162, A:Q.235, A:T.238, A:T.238, A:S.272, A:R.274, A:R.274 Water bridges: A:K.208 Salt bridges: A:R.150 pi-Stacking: A:F.165, A:F.165 pi-Cation interactions: A:R.274 ANP.19: 17 residues within 4Å: Chain B: R.150, E.152, F.159, I.160, R.161, S.162, F.165, W.167, Q.235, G.236, G.237, T.238, S.272, R.274, K.474 Ligands: HFG.20, MG.21 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:R.150, B:E.152, B:R.161, B:R.161, B:S.162, B:Q.235, B:T.238, B:T.238, B:S.272, B:R.274, B:R.274, B:K.474 Water bridges: B:K.208, B:K.208, B:K.208, B:K.208, B:K.208 Salt bridges: B:R.150 pi-Stacking: B:F.165, B:F.165 pi-Cation interactions: B:R.274

2 x HFG: 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one(Non-covalent)

HFG.2: 17 residues within 4Å: Chain A: F.95, E.98, V.99, P.118, T.119, E.121, R.150, W.167, E.169, H.171, F.214, T.238, H.240, S.268, W.269, G.270 Ligands: ANP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.95, A:T.119, A:W.167, A:E.169, A:F.214 Hydrogen bonds: A:T.119, A:T.119, A:R.150, A:S.268 Water bridges: A:R.150, A:H.240 pi-Stacking: A:F.95, A:F.95 HFG.20: 17 residues within 4Å: Chain B: F.95, E.98, V.99, P.118, T.119, E.121, R.150, W.167, E.169, H.171, F.214, T.238, H.240, S.268, W.269, G.270 Ligands: ANP.19 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.95, B:T.119, B:W.167, B:E.169, B:F.214 Hydrogen bonds: B:T.119, B:R.150, B:S.268 Water bridges: B:R.150, B:H.240 pi-Stacking: B:F.95, B:F.95

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: R.150 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain B: R.150 Ligands: ANP.19 No protein-ligand interaction detected (PLIP)

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

EDO.4: 4 residues within 4Å: Chain A: L.110, Q.111, E.112 Chain B: W.151 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain B: S.404, N.407 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain B: R.421, P.486 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain B: H.441, K.501 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: K.68, L.69, G.70 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: Y.38, Y.39, V.41, S.42, G.43, C.44, Y.45 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: R.375, E.380, W.382, K.400 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: F.22, S.23, Y.26, M.281, T.467, Y.513 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: W.151, R.163 Chain B: L.110, Q.111 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: K.154, K.474 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: R.294, K.395, L.398, D.399 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: Q.299, G.330, I.331, R.332, K.395 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: F.22, S.23, Y.26, M.281, T.467, Y.513 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: R.294, Q.299, K.395, L.398, D.399 Ligands: EDO.23 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: Q.299, G.330, K.395 Ligands: EDO.18 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: S.404, N.407 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain A: R.421, P.486 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain B: Y.38, Y.39, V.41, S.42, G.43, C.44, Y.45 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: R.375, E.380, W.382, K.400 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain A: T.342, P.343, G.344 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: W.131, L.140 Chain B: R.48, P.49 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 1 residues within 4Å: Chain A: K.130 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:K.130, B:D.37, B:D.37 Salt bridges: A:K.130 SO4.22: 5 residues within 4Å: Chain A: R.338, R.341, W.345, Y.349 Chain B: R.136 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.136, A:R.338, A:R.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with halofuginone and AMPPNP. TO BE PUBLISHED

Release Date

2019-11-27

Peptides

Prolyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Prolyl-tRNA synthetase

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