SMTL ID : 6rlv.1

Trypanosoma brucei Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: L.3, D.4, L.7, F.8, V.136, G.137, N.138, I.139, D.393, Q.397 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.4, A:G.137, A:I.139, A:D.393, A:Q.397 GOL.2: 5 residues within 4Å: Chain A: T.223, P.284, L.285, K.286, Y.287 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:K.199 Hydrogen bonds: A:T.223, A:K.286, A:K.286, A:Y.287 GOL.3: 6 residues within 4Å: Chain A: Y.272, H.273, R.276, F.278, Y.287 Chain B: K.199 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.273, B:K.199, B:K.199 Water bridges: A:R.276 GOL.4: 5 residues within 4Å: Chain A: E.176, M.181, D.182, T.183, S.184 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.181, A:D.182, A:T.183, A:S.184 Water bridges: A:M.181 GOL.8: 5 residues within 4Å: Chain B: W.277, T.279, G.404, P.405, N.406 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.406 Water bridges: B:N.406, B:N.406 GOL.9: 9 residues within 4Å: Chain B: L.3, D.4, F.8, V.136, G.137, N.138, I.139, D.393, Q.397 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.4, B:G.137, B:I.139, B:D.393, B:Q.397 GOL.10: 4 residues within 4Å: Chain B: R.276, W.277, F.278 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.276, B:W.277, B:W.277 GOL.11: 9 residues within 4Å: Chain A: K.199 Chain B: Y.272, H.273, R.276, F.278, L.285, Y.287 Ligands: GOL.10, GOL.12 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.272, B:H.273, B:Y.287, A:K.199, A:K.199 GOL.12: 6 residues within 4Å: Chain B: T.223, P.284, L.285, K.286, Y.287 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.223, B:K.286, B:K.286

6 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain A: K.369, E.384, S.387 Ligands: FZT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.369, A:E.384, A:S.387 NA.6: 3 residues within 4Å: Chain A: N.170, S.379, R.383 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.170, A:S.379, A:R.383 NA.13: 4 residues within 4Å: Chain B: K.369, E.384, S.387 Ligands: FZT.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.369, B:S.387, B:S.387 NA.14: 3 residues within 4Å: Chain B: L.407, T.410, Q.413 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.410 Water bridges: B:T.410 NA.15: 2 residues within 4Å: Chain B: N.162, T.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.162, B:T.164 NA.16: 2 residues within 4Å: Chain B: N.170, S.379 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.170, B:S.379

2 x FZT: 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine(Non-covalent)

FZT.7: 21 residues within 4Å: Chain A: T.264, E.266, R.295, E.297, F.309, R.310, V.311, F.314, K.316, E.318, E.384, L.385, V.386, S.387, N.423, G.424, T.425, A.428, T.430, R.431 Ligands: NA.5 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.266, A:E.266, A:R.295, A:V.311, A:K.316, A:S.387, A:S.387, A:T.425, A:R.431, A:R.431, A:R.431 Water bridges: A:R.295, A:R.295, A:S.387, A:R.431 Salt bridges: A:R.295 pi-Stacking: A:F.314 pi-Cation interactions: A:R.431 FZT.17: 21 residues within 4Å: Chain B: T.264, E.266, R.295, E.297, F.309, R.310, V.311, F.314, K.316, E.318, E.384, L.385, V.386, S.387, N.423, G.424, T.425, A.428, T.430, R.431 Ligands: NA.13 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.264, B:E.266, B:R.295, B:V.311, B:K.316, B:E.384, B:S.387, B:T.425, B:T.425, B:T.425, B:R.431, B:R.431, B:R.431 Water bridges: B:R.295, B:R.295, B:R.431 Salt bridges: B:R.295 pi-Stacking: B:F.314 pi-Cation interactions: B:R.431

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.18: 6 residues within 4Å: Chain B: W.277, R.402, N.406, L.407, R.408, K.416 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.406, B:L.407, B:R.408 Salt bridges: B:R.402, B:K.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, L. et al., Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases. Acs Chem.Biol. (2020)

Release Date

2020-01-08

Peptides

Seryl-tRNA synthetase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Seryl-tRNA synthetase, putative

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