SMTL ID : 3g1z.1

Structure of IDP01693/yjeA, a potential t-RNA synthetase from Salmonella typhimurium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 16 residues within 4Å: Chain A: R.101, E.103, H.108, H.109, N.110, F.113, M.115, E.245, L.246, A.247, N.248, A.299, G.301, R.304, L.315 Ligands: PO4.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.101, A:E.103, A:N.110, A:E.245, A:G.301, A:R.304 Water bridges: A:D.303 Salt bridges: A:R.101 pi-Stacking: A:F.113, A:F.113 AMP.5: 15 residues within 4Å: Chain B: R.101, E.103, H.108, H.109, N.110, F.113, E.245, L.246, A.247, N.248, A.299, G.301, R.304, L.315 Ligands: PO4.8 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.101, B:E.103, B:N.110, B:E.245, B:N.248, B:G.301, B:R.304 Water bridges: B:R.101, B:R.101, B:E.238, B:D.303 Salt bridges: B:R.101 pi-Stacking: B:F.113, B:F.113

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

PO4.2: 4 residues within 4Å: Chain A: G.106, R.107, H.108, H.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.107, A:H.108, A:H.109 Salt bridges: A:H.108, A:H.109 PO4.3: 6 residues within 4Å: Chain A: M.125, Y.126, H.215, S.227, E.229, E.235 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.227 Water bridges: A:M.125, A:Y.126, A:S.227, A:T.228, A:E.235 Salt bridges: A:H.215 PO4.4: 4 residues within 4Å: Chain A: H.109, E.245, R.304 Ligands: AMP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.245, A:E.245 Water bridges: A:R.101 Salt bridges: A:H.109, A:R.304 PO4.6: 4 residues within 4Å: Chain B: G.106, R.107, H.108, H.109 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.107, B:H.108, B:H.109 Salt bridges: B:R.107, B:H.108, B:H.109 PO4.7: 5 residues within 4Å: Chain B: Y.126, H.215, S.227, E.229, E.235 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Y.126, B:I.226, B:S.227, B:T.228 Salt bridges: B:H.215 PO4.8: 4 residues within 4Å: Chain B: H.109, E.245, R.304 Ligands: AMP.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.245, B:E.245 Water bridges: B:R.101, B:E.103 Salt bridges: B:H.109, B:R.304

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 1 residues within 4Å: Chain B: R.34 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Navarre, W.W. et al., PoxA, yjeK, and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica. Mol.Cell (2010)

Release Date

2009-03-10

Peptides

Putative lysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative lysyl-tRNA synthetase