SMTL ID : 3jxe.1

Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase in complex with TrpAMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x TYM: TRYPTOPHANYL-5'AMP(Non-covalent)

TYM.1: 25 residues within 4Å: Chain A: Y.77, T.78, G.79, R.80, G.81, G.89, H.90, P.93, Q.111, T.113, E.116, K.117, Q.198, I.211, A.213, A.214, D.216, Q.217, W.221, K.242, F.243, V.244, K.253, M.254 Ligands: SO4.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.113, A:I.211, A:A.213, A:Q.217, A:W.221 Hydrogen bonds: A:Y.77, A:G.81, A:Q.198, A:Q.198, A:A.214, A:D.216, A:V.244, A:V.244, A:K.253, A:M.254 Salt bridges: A:R.80, A:H.90, A:K.117, A:K.117 TYM.3: 25 residues within 4Å: Chain B: Y.77, T.78, G.79, R.80, G.81, G.89, H.90, P.93, Q.111, T.113, E.116, K.117, Q.198, I.211, A.213, A.214, D.216, Q.217, W.221, K.242, F.243, V.244, K.253, M.254 Ligands: SO4.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.211, B:A.213, B:Q.217, B:W.221 Hydrogen bonds: B:Y.77, B:G.81, B:G.81, B:Q.198, B:Q.198, B:A.214, B:D.216, B:V.244, B:V.244, B:K.253, B:M.254 Salt bridges: B:R.80, B:H.90, B:K.117, B:K.117

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

SO4.2: 7 residues within 4Å: Chain A: H.87, H.90, K.253, M.254, S.255, A.256 Ligands: TYM.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.254, A:A.256 Salt bridges: A:H.87, A:H.90, A:K.253 SO4.4: 7 residues within 4Å: Chain B: H.87, H.90, K.253, M.254, S.255, A.256 Ligands: TYM.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.255, B:A.256 Salt bridges: B:H.87, B:H.90, B:K.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, M. et al., Crystal structure of P. horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase. To be Published

Release Date

2009-11-10

Peptides

Tryptophanyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophanyl-tRNA synthetase