SMTL ID : 3qo8.1

Crystal Structure of seryl-tRNA synthetase from Candida albicans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x SSA: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE(Non-covalent)

SSA.1: 19 residues within 4Å: Chain A: T.246, E.248, R.279, E.281, F.293, R.294, V.295, F.298, K.300, E.302, E.366, L.367, V.368, S.369, N.402, T.404, A.407, R.410 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.246, A:R.279, A:E.281, A:V.295, A:K.300, A:E.302, A:E.366, A:E.366, A:S.369, A:T.404, A:R.410, A:R.410 Water bridges: A:R.279, A:R.279, A:R.294, A:S.369, A:A.407 Salt bridges: A:R.279 pi-Stacking: A:F.298, A:F.298 pi-Cation interactions: A:R.410, A:R.410 SSA.3: 15 residues within 4Å: Chain A: W.131, P.133, E.134, A.145, Q.328, S.329, L.330, G.331, Y.419, V.426, I.427, P.428, E.429, V.430, R.432 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.134, A:E.134, A:A.145, A:E.429, A:V.430, A:R.432 Water bridges: A:E.429, A:R.432 pi-Stacking: A:Y.419, A:Y.419 SSA.5: 19 residues within 4Å: Chain B: T.246, E.248, R.279, E.281, F.293, R.294, V.295, F.298, K.300, E.302, E.366, L.367, V.368, S.369, N.402, T.404, A.407, R.410 Ligands: MG.6 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:E.248, B:R.279, B:E.281, B:V.295, B:K.300, B:E.302, B:E.366, B:S.369, B:T.404, B:R.410, B:R.410 Water bridges: B:R.279, B:R.279, B:R.294, B:S.369, B:A.407 Salt bridges: B:R.279 pi-Stacking: B:F.298, B:F.298 pi-Cation interactions: B:R.410, B:R.410 SSA.7: 15 residues within 4Å: Chain B: W.131, P.133, E.134, A.145, Q.328, S.329, L.330, G.331, Y.419, V.426, I.427, P.428, E.429, V.430, R.432 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:E.134, B:A.145, B:Y.419, B:E.429, B:V.430, B:R.432 Water bridges: B:E.429, B:E.429, B:R.432 pi-Stacking: B:Y.419, B:Y.419

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.366, S.369 Ligands: SSA.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.366, A:S.369, H2O.3, H2O.9, H2O.10 MG.4: 1 residues within 4Å: Chain A: L.344 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:L.344, H2O.1, H2O.1, H2O.1, H2O.4, H2O.5 MG.6: 3 residues within 4Å: Chain B: E.366, S.369 Ligands: SSA.5 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.366, B:S.369, H2O.13, H2O.19, H2O.20 MG.8: 1 residues within 4Å: Chain B: L.344 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:L.344, H2O.11, H2O.11, H2O.11, H2O.14, H2O.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocha, R. et al., Unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-08-03

Peptides

Seryl-tRNA synthetase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Seryl-tRNA synthetase, cytoplasmic

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