SMTL ID : 4eg4.2 (1 other biounit)

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1289

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

monomer

Ligands

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

DMS.1: 3 residues within 4Å: Chain A: F.88, Y.93, I.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.95 DMS.10: 2 residues within 4Å: Chain A: Y.241 Ligands: 0OT.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.241

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.40, R.43, V.44, S.483, P.487, K.505 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.40, A:R.43, A:S.483 GOL.3: 6 residues within 4Å: Chain A: E.112, L.113, K.116, L.251, R.255, D.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.112, A:R.255, A:D.269 Water bridges: A:D.270 GOL.4: 2 residues within 4Å: Chain A: R.352, R.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.352, A:R.370 GOL.5: 3 residues within 4Å: Chain A: K.111, P.233, G.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.234 GOL.6: 4 residues within 4Å: Chain A: H.58, K.107, W.228, A.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.58, A:K.107, A:A.229 GOL.7: 5 residues within 4Å: Chain A: G.342, Y.343, D.344, A.345, K.489 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.343, A:D.344, A:A.345 Water bridges: A:K.489, A:K.489 GOL.8: 3 residues within 4Å: Chain A: K.69, V.71, A.79 No protein-ligand interaction detected (PLIP) GOL.9: 2 residues within 4Å: Chain A: E.204, K.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.204

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

SO4.11: 5 residues within 4Å: Chain A: I.17, Y.18, Y.19, H.28 Ligands: 0OT.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.17, A:Y.19 Salt bridges: A:H.28

1 x 0OT: 2-({3-[(3,5-dibromo-2-ethoxybenzyl)amino]propyl}amino)quinolin-4(1H)-one(Non-covalent)

0OT.12: 19 residues within 4Å: Chain A: P.16, I.17, Y.19, D.56, H.58, G.59, L.225, V.240, Y.241, V.242, W.243, D.245, A.246, L.247, Y.250, I.288, H.292 Ligands: DMS.10, SO4.11 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.19, A:Y.19, A:H.58, A:L.225, A:Y.241, A:V.242, A:W.243, A:D.245, A:A.246, A:L.247, A:I.288, A:I.288 Hydrogen bonds: A:D.56, A:D.56 Water bridges: A:Y.241 Halogen bonds: A:Y.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koh, C.Y. et al., Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection. Structure (2012)

Release Date

2012-09-12

Peptides

Methionyl-tRNA synthetase, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Methionyl-tRNA synthetase, putative

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