SMTL ID : 4yrp.1

Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 1-(4-BROMOPHENYL)METHANAMINE (Chem 707)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: H.1, A:E.104, A:T.106, A:Q.148, A:D.152, A:Y.297, A:Y.297 Water bridges: A:T.106, A:R.292 HIS.9: 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: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:E.104, B:E.104, B:T.106, B:Q.148, B:D.152, B:Y.296, B:Y.297, B:Y.297, H.9 Water bridges: B:T.106, B:R.292, B:G.339, B:G.339

2 x PZH: 1-(4-BROMOPHENYL)METHANAMINE(Non-covalent)

PZH.2: 8 residues within 4Å: Chain A: C.132, W.133, R.134, R.143, R.144, E.145, H.146 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.146 Hydrogen bonds: A:R.144, A:H.146 pi-Stacking: A:H.146 PZH.10: 7 residues within 4Å: Chain B: C.132, W.133, R.134, R.144, E.145, H.146 Ligands: SO4.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:H.146 Hydrogen bonds: B:R.144 pi-Stacking: B:H.146

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 4 residues within 4Å: Chain A: W.171, R.174, S.175, Y.280 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.171, A:W.171 DMS.4: 5 residues within 4Å: Chain A: E.74, L.75, I.77, R.78, Y.327 No protein-ligand interaction detected (PLIP) DMS.11: 3 residues within 4Å: Chain B: W.171, R.174, S.175 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:W.171 DMS.12: 7 residues within 4Å: Chain A: V.27 Chain B: E.74, L.75, I.77, R.78, T.326, Y.327 No protein-ligand interaction detected (PLIP) DMS.13: 3 residues within 4Å: Chain B: V.450, P.451, R.454 No protein-ligand interaction detected (PLIP) DMS.14: 3 residues within 4Å: Chain B: I.213, V.231, L.232 No protein-ligand interaction detected (PLIP)

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

EDO.5: 6 residues within 4Å: Chain A: T.93, K.94, G.95, H.97 Chain B: Y.135, R.144 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.144, B:R.144, A:T.93 EDO.15: 6 residues within 4Å: Chain A: Y.135, R.144 Chain B: T.93, K.94, G.95, H.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.93, B:T.93, B:H.97

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

SO4.6: 6 residues within 4Å: Chain A: H.146, G.341, D.342, C.343, V.344 Ligands: PZH.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.342, A:D.342, A:C.343, A:V.344 Water bridges: A:G.341, A:I.345 Salt bridges: A:H.146 SO4.7: 4 residues within 4Å: Chain A: R.47, F.50, H.54 Chain B: R.47 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.47, A:H.54, B:R.47 Water bridges: B:R.47, B:R.47 SO4.8: 4 residues within 4Å: Chain A: R.174, S.179, S.180, W.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.180, A:S.180 Salt bridges: A:R.174 SO4.16: 4 residues within 4Å: Chain B: R.174, S.179, S.180, W.283 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.180 Water bridges: B:R.174 Salt bridges: B:R.174 SO4.17: 6 residues within 4Å: Chain B: H.146, G.341, D.342, C.343, V.344 Ligands: PZH.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.342, B:C.343, B:V.344 Water bridges: B:G.341, B:G.341, B:I.345 Salt bridges: B:H.146

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
B

Histidyl-tRNA synthetase

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