SMTL ID : 3a32.1

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.7, Y.12, E.392, S.393, K.396 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.331 Salt bridges: A:K.7, A:K.396 SO4.2: 4 residues within 4Å: Chain A: K.203, R.205, V.248, E.275 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.203, A:R.205 SO4.3: 2 residues within 4Å: Chain A: K.406, R.427 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.406, A:R.427 SO4.4: 5 residues within 4Å: Chain A: D.164, H.310, R.311, A.312 Ligands: ZN.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.311 Water bridges: A:Q.162, A:Q.162 SO4.5: 5 residues within 4Å: Chain A: E.190, K.194, L.195, G.196, E.421 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.421 Salt bridges: A:K.194 SO4.7: 5 residues within 4Å: Chain B: K.7, Y.12, E.392, S.393, K.396 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.12 Water bridges: B:R.331 Salt bridges: B:K.7, B:K.396 SO4.8: 4 residues within 4Å: Chain B: K.203, R.205, V.248, E.275 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.203, B:R.205 SO4.9: 2 residues within 4Å: Chain B: K.406, R.427 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.406, B:R.427 SO4.10: 5 residues within 4Å: Chain B: D.164, H.310, R.311, A.312 Ligands: ZN.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.164, B:R.311 Water bridges: B:Q.162, B:Q.162 SO4.11: 5 residues within 4Å: Chain B: E.190, K.194, L.195, G.196, E.421 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.421 Salt bridges: B:K.194

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.112, H.166, H.310 Ligands: SO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.112, A:H.166, A:H.310, H2O.8 ZN.12: 4 residues within 4Å: Chain B: C.112, H.166, H.310 Ligands: SO4.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.112, B:H.166, B:H.310, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimizu, S. et al., Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain. J.Mol.Biol. (2009)

Release Date

2009-10-27

Peptides

Probable threonyl-tRNA synthetase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Probable threonyl-tRNA synthetase 1

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