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

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor Chem 1320

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: E.406, D.450 No protein-ligand interaction detected (PLIP) GOL.2: 6 residues within 4Å: Chain A: E.112, K.116, L.251, R.255, D.269, F.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.112, A:R.255 GOL.3: 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.4: 2 residues within 4Å: Chain A: R.177, A.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.177 Water bridges: A:D.122, A:R.184 GOL.5: 5 residues within 4Å: Chain A: R.40, R.43, S.483, P.487, K.505 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:R.43 GOL.6: 4 residues within 4Å: Chain A: A.401, A.402, E.462, R.463 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.402 GOL.7: 6 residues within 4Å: Chain A: H.58, Y.74, T.102, K.107, W.228, A.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.58, A:T.102, A:K.107 GOL.8: 3 residues within 4Å: Chain A: G.1, Q.412, K.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.1, A:Q.412, A:K.415

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

DMS.9: 3 residues within 4Å: Chain A: Y.93, S.94, 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, W.243 No protein-ligand interaction detected (PLIP) DMS.11: 3 residues within 4Å: Chain A: Y.343, D.344, K.489 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.344, A:K.489 Salt bridges: A:D.344

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

SO4.12: 4 residues within 4Å: Chain A: Y.18, Y.19, H.28 Ligands: 0P8.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.19 Salt bridges: A:H.28

1 x 0P8: 2-({3-[(3,5-dibromo-2-methoxybenzyl)amino]propyl}amino)quinolin-4(1H)-one(Non-covalent)

0P8.13: 19 residues within 4Å: Chain A: I.17, Y.19, D.56, H.58, G.59, E.137, 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: SO4.12 14 PLIP interactions: 14 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 Hydrogen bonds: A:D.56, A:D.56, A:D.56 Water bridges: A:Y.19 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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