SMTL ID : 4yrt.1

Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with N-(5-hydroxynaphthalen-2-yl)propanamide (Chem 1781)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x HIS: HISTIDINE(Non-covalent)

HIS.1: 13 residues within 4Å: Chain A: E.104, T.106, Q.148, N.150, D.152, L.294, Y.296, Y.297, G.316, Y.320, G.337, F.338, G.339 13 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:E.104, A:E.104, A:T.106, A:Q.148, A:D.152, A:R.292, A:Y.296, H.1, H.1 Water bridges: A:T.106, A:Y.297, A:G.339, A:G.339 HIS.5: 13 residues within 4Å: Chain B: E.104, T.106, Q.148, N.150, D.152, L.294, Y.296, Y.297, G.316, Y.320, G.337, F.338, G.339 13 PLIP interactions: 11 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:E.104, B:E.104, B:E.104, B:T.106, B:Q.148, B:D.152, B:R.292, B:Y.297, H.5, H.5 Water bridges: B:T.106, B:G.339, B:G.339

2 x 781: N-(5-hydroxynaphthalen-2-yl)propanamide(Covalent)

781.2: 10 residues within 4Å: Chain A: C.132, W.133, R.134, R.142, R.144, E.145, H.146, C.343, V.344, E.347 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.134, A:R.134, A:H.146, A:V.344 Hydrogen bonds: A:R.134, A:R.142 Water bridges: A:P.103, A:H.146, A:C.343 pi-Stacking: A:H.146, A:H.146 781.6: 10 residues within 4Å: Chain B: C.132, W.133, R.134, R.142, R.144, E.145, H.146, C.343, V.344, E.347 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.134, B:R.134, B:H.146, B:V.344 Hydrogen bonds: B:R.134, B:R.142 Water bridges: B:P.103, B:H.146, B:H.146, B:C.343 pi-Stacking: B:H.146, B:H.146

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

SO4.3: 5 residues within 4Å: Chain A: R.47 Chain B: R.47, F.50, H.54 Ligands: SO4.7 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Water bridges: B:R.46, B:R.46, B:R.47, A:R.46 Salt bridges: B:R.47, B:H.54, A:R.47 SO4.7: 5 residues within 4Å: Chain A: R.47, F.50, H.54 Chain B: R.47 Ligands: SO4.3 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:R.46, A:R.46, A:R.46, A:R.47 Salt bridges: B:R.47, A:R.47, A:H.54

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

EDO.4: 5 residues within 4Å: Chain A: T.93, G.95, H.97 Chain B: Y.135, R.144 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.93, A:G.95, B:Y.135, B:R.144, B:R.144 EDO.8: 5 residues within 4Å: Chain A: Y.135, R.144 Chain B: T.93, G.95, H.97 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.93, B:T.93, B:G.95, A:R.144, A:R.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koh, C.Y. et al., A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens. Acta Crystallogr. D Biol. Crystallogr. (2015)

Release Date

2015-08-12

Peptides

Histidyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histidyl-tRNA synthetase

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