SMTL ID : 4iko.1

Structure of Peptidyl- tRNA Hydrolase from Acinetobacter baumannii at 1.90 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: P.13, G.14, F.26, E.30, M.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.14, A:E.30 Water bridges: A:E.30, A:E.30 GOL.6: 3 residues within 4Å: Chain A: E.16, Y.17, L.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.150 Water bridges: A:Y.17, A:Y.17 GOL.8: 2 residues within 4Å: Chain A: N.70, R.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.70, A:R.71 Water bridges: A:N.70

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: K.45, F.46, P.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.45, A:K.45 EDO.3: 5 residues within 4Å: Chain A: D.43, P.44, H.47, G.48, M.66 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.43, A:G.48, A:G.48 Water bridges: A:H.47, A:M.66

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 8 residues within 4Å: Chain A: E.96, K.107, G.111, H.112, G.113, L.118, R.131, R.133 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.96 Water bridges: A:R.131, A:R.131 Salt bridges: A:K.107, A:R.131, A:R.133

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 4 residues within 4Å: Chain A: Y.36, N.54, I.55, E.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.56 PEG.7: 7 residues within 4Å: Chain A: Y.36, G.37, I.38, T.39, R.52, G.53, N.54 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.36, A:T.39, A:N.54 Water bridges: A:T.39, A:T.39, A:R.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaushik, S. et al., The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii. Plos One (2013)

Release Date

2013-01-30

Peptides

Peptidyl-tRNA hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidyl-tRNA hydrolase

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