SMTL ID : 4eg4.1 (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

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: W.114, E.118, Y.174, V.232, P.233, G.234, N.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.114, A:E.118 GOL.2: 6 residues within 4Å: Chain A: R.40, V.44, S.483, P.487, S.490, V.491 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:P.487, A:S.490 GOL.3: 4 residues within 4Å: Chain A: V.499, P.500, E.501, R.504 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.501, A:R.504 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.352 GOL.5: 2 residues within 4Å: Chain A: H.164, V.165 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.165 GOL.6: 4 residues within 4Å: Chain A: K.45, G.419, D.422, F.510 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.45 Water bridges: A:K.45, A:D.422 GOL.7: 2 residues within 4Å: Chain A: P.214, D.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.215 GOL.8: 6 residues within 4Å: Chain A: G.342, Y.343, D.344, A.345, R.488, K.489 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.344, A:A.345, A:K.489 GOL.9: 8 residues within 4Å: Chain A: Y.30, S.354, G.355, F.356, P.428, D.429, I.430, Q.431 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.355, A:P.428, A:D.429, A:I.430, A:Q.431 GOL.10: 7 residues within 4Å: Chain A: N.21, A.22, H.25, K.61, K.319, D.320, R.321 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.28, A:K.61, A:K.61, A:D.320, A:R.321 GOL.11: 3 residues within 4Å: Chain A: P.500, H.503, P.516 No protein-ligand interaction detected (PLIP) GOL.16: 5 residues within 4Å: Chain A: P.198, E.199, F.356, D.429, K.432 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.199, A:D.429, A:K.432

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

DMS.12: 5 residues within 4Å: Chain A: A.208, K.290, I.294 Ligands: DMS.13, DMS.15 No protein-ligand interaction detected (PLIP) DMS.13: 7 residues within 4Å: Chain A: E.161, K.286, D.287, I.288, L.289, K.290 Ligands: DMS.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.289, A:K.290 Salt bridges: A:E.161 DMS.14: 6 residues within 4Å: Chain A: F.139, P.214, L.216, K.290, Y.295 Ligands: DMS.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.295 DMS.15: 3 residues within 4Å: Chain A: K.290 Ligands: DMS.12, DMS.14 No protein-ligand interaction detected (PLIP)

1 x MET: METHIONINE(Non-covalent)

MET.17: 14 residues within 4Å: Chain A: P.16, I.17, Y.18, Y.19, D.56, W.243, A.246, L.247, N.249, Y.250, I.288, H.292, T.318, K.319 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.243 Hydrogen bonds: A:Y.19, A:D.56 Salt bridges: A:K.319

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
A

Methionyl-tRNA synthetase, putative

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