SMTL ID : 4eg5.2 (1 other biounit)

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1312

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: E.112, L.113, K.116, L.251, R.255, D.269, F.271, L.305 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.112, A:K.116, A:R.255, A:F.271 Water bridges: A:D.270 GOL.2: 2 residues within 4Å: Chain A: R.352, R.370 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.352, A:R.352, A:R.370, A:R.370 GOL.3: 2 residues within 4Å: Chain A: R.177, A.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.177, A:R.177 GOL.4: 5 residues within 4Å: Chain A: R.40, R.43, V.44, S.483 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:R.43 GOL.5: 4 residues within 4Å: Chain A: G.342, Y.343, D.344, K.489 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.343, A:D.344, A:D.344, A:K.489 GOL.6: 2 residues within 4Å: Chain A: E.406, D.450 No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain A: R.40, D.92, R.488 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.40, A:D.92, A:R.488

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

DMS.8: 2 residues within 4Å: Chain A: F.291 Ligands: 0OU.10 No protein-ligand interaction detected (PLIP)

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

SO4.9: 4 residues within 4Å: Chain A: Y.18, Y.19, H.28 Ligands: 0OU.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.19 Salt bridges: A:H.28

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

0OU.10: 20 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, F.291, H.292 Ligands: DMS.8, SO4.9 15 PLIP interactions: 15 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:A.246, A:L.247, A:I.288, A:I.288, A:F.291 Hydrogen bonds: A:D.56, A:D.56 Water bridges: A:Q.60 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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