SMTL ID : 3svj.1

Strep Peptide Deformylase with a time dependent thiazolidine amide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: S.118, R.146 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.119, A:V.119 Salt bridges: A:R.146 SO4.2: 2 residues within 4Å: Chain A: K.9, A.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.10 Salt bridges: A:K.9 SO4.3: 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 4LI: (4R)-3-(4-[4-(2-CHLOROPHENYL)PIPERAZIN-1-YL]-6-{[2-METHYL-6-(METHYLCARBAMOYL)PHENYL]AMINO}-1,3,5-TRIAZIN-2-YL)-N-METHYL-1,3-THIAZOLIDINE-4-CARBOXAMIDE(Non-covalent)

4LI.4: 12 residues within 4Å: Chain A: Q.57, G.69, G.70, V.71, G.72, E.126, G.127, E.128, G.129, C.130, L.131, H.173 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.126 Hydrogen bonds: A:V.71, A:G.72, A:E.126, A:G.127, A:G.129, A:G.129 Water bridges: A:L.131

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

NI.5: 4 residues within 4Å: Chain A: Q.77, C.130, H.173, H.177 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.173, A:H.177, H2O.4, H2O.4

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: S.116, H.117, S.118, R.146, V.147, T.148, K.162 Ligands: SO4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.116, A:H.117, A:V.147, A:T.148 Water bridges: A:L.163

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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