SMTL ID : 3lss.1

Trypanosoma brucei seryl-tRNA synthetase in complex with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: R.300, E.302, F.314, R.315, V.316, F.319, K.321, K.374, E.389, L.390, V.391, S.392, T.430, A.433, T.435, R.436 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:E.302, A:V.316, A:E.389, A:E.389, A:E.389, A:E.389, A:S.392 Water bridges: A:K.374 Salt bridges: A:R.300, A:R.300, A:K.374 pi-Stacking: A:F.319 pi-Cation interactions: A:R.436, A:R.436 ATP.5: 17 residues within 4Å: Chain B: R.300, E.302, F.314, R.315, V.316, F.319, K.321, K.374, D.376, E.389, L.390, V.391, S.392, T.430, A.433, T.435, R.436 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.302, B:V.316, B:E.389, B:E.389, B:S.392, B:R.436 Water bridges: B:R.315, B:K.321, B:K.374, B:K.374 Salt bridges: B:R.300, B:R.300, B:K.374 pi-Stacking: B:F.319 pi-Cation interactions: B:R.436, B:R.436

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

MLI.2: 7 residues within 4Å: Chain A: V.212, V.215, M.295, D.320 Chain B: V.215, M.295, D.320 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.211, B:Q.211 MLI.3: 3 residues within 4Å: Chain A: R.281, W.282, F.283 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.281 Hydrogen bonds: A:W.282 Salt bridges: A:R.281

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

NA.4: 2 residues within 4Å: Chain A: N.167, T.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.167, A:T.169 Water bridges: A:T.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larson, E.T. et al., X-ray crystal structure of Seryl-tRNA synthetase from the eukaryotic parasite Trypanosoma brucei. to be published

Release Date

2010-03-02

Peptides

Seryl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Seryl-tRNA synthetase

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