SMTL ID : 2dq0.1

Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with a seryl-adenylate analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: S.183, R.184, T.288, A.289, H.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.183, A:S.183 Salt bridges: A:R.184, A:H.300 SO4.2: 6 residues within 4Å: Chain A: K.291, D.292, T.293, R.298, R.369 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.292, A:T.293 Salt bridges: A:R.298, A:R.369 SO4.3: 6 residues within 4Å: Chain A: F.297, R.298, R.369, E.370, R.412 Ligands: SO4.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.370, A:E.370, A:E.370 Water bridges: A:R.369, A:R.369 Salt bridges: A:R.298, A:R.369, A:R.412 SO4.4: 4 residues within 4Å: Chain A: A.172, D.173, F.174, A.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.173, A:F.174, A:A.175 SO4.6: 5 residues within 4Å: Chain B: S.183, R.184, T.288, A.289, H.300 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.183, B:S.183, B:T.288 Salt bridges: B:R.184, B:H.300 SO4.7: 6 residues within 4Å: Chain B: K.291, D.292, T.293, F.297, R.298, R.369 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.292, B:T.293, B:T.293 Salt bridges: B:K.291, B:R.298, B:R.369 SO4.8: 5 residues within 4Å: Chain B: F.297, R.298, R.369, E.370, R.412 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.369 Water bridges: B:R.298, B:E.370, B:E.370, B:E.370, B:R.412 Salt bridges: B:R.298, B:R.412

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

SSA.5: 20 residues within 4Å: Chain A: T.252, E.254, R.283, E.285, F.297, R.298, V.299, F.302, K.304, E.306, E.370, V.371, V.372, S.373, N.404, S.405, T.406, A.409, S.411, R.412 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.252, A:T.252, A:E.254, A:R.283, A:E.285, A:V.299, A:K.304, A:E.370, A:V.371, A:S.373, A:S.373, A:T.406, A:S.411 Water bridges: A:A.409 Salt bridges: A:R.283 pi-Stacking: A:F.302, A:F.302 pi-Cation interactions: A:R.412, A:R.412 SSA.9: 19 residues within 4Å: Chain B: T.252, E.254, R.283, E.285, F.297, R.298, V.299, F.302, K.304, E.306, E.370, V.371, V.372, S.373, N.404, T.406, A.409, S.411, R.412 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:R.283, B:R.283, B:E.285, B:E.285, B:V.299, B:K.304, B:K.304, B:E.370, B:E.370, B:V.371, B:S.373, B:S.373, B:S.373, B:T.406, B:S.411 Water bridges: B:A.409 Salt bridges: B:R.283 pi-Stacking: B:F.302, B:F.302 pi-Cation interactions: B:R.412, B:R.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itoh, Y. et al., Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii. Rna Biol. (2008)

Release Date

2007-06-05

Peptides

Seryl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Seryl-tRNA synthetase

Related Entries With Identical Sequence