SMTL ID : 5jf3.1

Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT018

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x SF5: methyl 4-({5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl}methyl)benzoate(Non-covalent)

SF5.1: 13 residues within 4Å: Chain A: G.69, G.70, V.71, G.72, Q.77, E.129, G.130, C.131, L.132, H.174, E.175, H.178 Ligands: ZN.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.132, A:H.174 Hydrogen bonds: A:V.71, A:G.72, A:Q.77, A:L.132

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

ACT.2: 5 residues within 4Å: Chain A: H.145, Q.173, D.177, R.187 Ligands: ZN.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.173 Water bridges: A:Q.173, A:R.187 Salt bridges: A:H.145, A:R.187

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 2 residues within 4Å: Chain A: E.32 Ligands: ZN.12 No protein-ligand interaction detected (PLIP)

9 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: Q.77, C.131, H.174, H.178 Ligands: SF5.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.174, A:H.178 ZN.5: 1 residues within 4Å: Chain A: H.55 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.55, H2O.7 ZN.6: 1 residues within 4Å: Chain A: H.118 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.118, H2O.7, H2O.8, H2O.8 ZN.7: 1 residues within 4Å: Chain A: E.190 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.190, A:E.190, H2O.2, H2O.5 ZN.8: 2 residues within 4Å: Chain A: H.145 Ligands: ACT.2 3 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.145, ACT.2, H2O.8 ZN.9: 4 residues within 4Å: Chain A: H.12, L.13, D.15, D.18 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.12, A:D.18, H2O.1, H2O.1, H2O.7 ZN.10: 3 residues within 4Å: Chain A: E.43, E.47, K.155 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.43, A:E.47, H2O.6 ZN.11: 3 residues within 4Å: Chain A: E.151, K.159, R.161 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.151, A:E.151, H2O.7, H2O.8, H2O.8 ZN.12: 2 residues within 4Å: Chain A: E.32 Ligands: IMD.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.32, H2O.1, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fieulaine, S. et al., A unique peptide deformylase platform to rationally design and challenge novel active compounds. Sci Rep (2016)

Release Date

2016-11-30

Peptides

Peptide deformylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide deformylase

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