SMTL ID : 3str.1

Strep Peptide Deformylase with a time dependent thiazolidine hydroxamic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 5 residues within 4Å: Chain A: Q.77, C.130, H.173, H.177 Ligands: 3LI.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.130, A:H.173, A:H.177

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

SO4.2: 3 residues within 4Å: Chain A: S.118, R.146 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.119 Salt bridges: A:R.146 SO4.3: 3 residues within 4Å: Chain A: E.106, A.107, I.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.108 SO4.4: 2 residues within 4Å: Chain A: K.9, A.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.10 Water bridges: A:A.11 SO4.5: 2 residues within 4Å: Chain A: H.144, R.186 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.144, A:R.186

1 x 3LI: (4R)-3-(4-[4-(2-chlorophenyl)piperazin-1-yl]-6-{[2-methyl-6-(methylcarbamoyl)phenyl]amino}-1,3,5-triazin-2-yl)-N-[2-(hydroxyamino)-2-oxoethyl]-1,3-thiazolidine-4-carboxamide(Non-covalent)

3LI.6: 18 residues within 4Å: Chain A: Q.57, G.69, G.70, V.71, G.72, Q.77, E.126, G.127, E.128, G.129, C.130, L.131, Y.166, I.169, H.173, E.174, H.177 Ligands: NI.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.57, A:E.126 Hydrogen bonds: A:V.71, A:G.72, A:G.72, A:Q.77, A:E.126, A:G.127, A:G.129, A:G.129, A:L.131

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: S.116, R.146, V.147, T.148, K.162 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.116, A:V.147, A:T.148 Water bridges: A:V.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Totoritis, R. et al., Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors. Biochemistry (2011)

Release Date

2011-07-27

Peptides

Peptide deformylase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

Peptide deformylase 3

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