SMTL ID : 4l87.1

Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

SSA.1: 20 residues within 4Å: Chain A: T.270, E.272, R.301, E.303, F.315, R.316, V.317, F.320, K.322, E.324, E.390, L.391, V.392, S.393, N.426, T.428, A.431, T.433, R.434 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:E.272, A:R.301, A:E.303, A:V.317, A:K.322, A:E.390, A:S.393, A:N.426, A:T.433, A:R.434 Salt bridges: A:R.301 pi-Stacking: A:F.320 pi-Cation interactions: A:R.434, A:R.434 SSA.5: 20 residues within 4Å: Chain B: T.270, E.272, R.301, E.303, F.315, R.316, V.317, F.320, K.322, E.324, E.390, L.391, V.392, S.393, N.426, T.428, A.431, T.433, R.434 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.270, B:R.301, B:E.303, B:V.317, B:K.322, B:E.390, B:E.390, B:S.393, B:N.426, B:T.433, B:R.434 Salt bridges: B:R.301 pi-Stacking: B:F.320 pi-Cation interactions: B:R.434, B:R.434

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: R.309, F.315, R.316, R.389, E.390 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.390 Salt bridges: A:R.309, A:R.316, A:R.389 PO4.6: 5 residues within 4Å: Chain B: R.309, F.315, R.316, R.389, E.390 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.390 Salt bridges: B:R.309, B:R.316, B:R.389

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.375, D.377, E.390 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: E.245, T.270, R.301 Ligands: SSA.1 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: K.375, D.377, E.390 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: E.245, T.270, R.301 Ligands: SSA.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X. et al., Crystal Structure of Human Seryl-tRNA Synthetase and Ser-SA Complex Reveals a Molecular Lever Specific to Higher Eukaryotes. Structure (2013)

Release Date

2013-10-02

Peptides

Serine--tRNA ligase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine--tRNA ligase, cytoplasmic