SMTL ID : 8rhr.1

E.coli Peptide Deformylase with bound inhibitor BB4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.53, C.93, H.135, H.139 Ligands: BB4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.93, A:H.135, A:H.139

1 x BB4: 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide(Non-covalent)

BB4.2: 18 residues within 4Å: Chain A: G.46, I.47, G.48, L.49, A.50, Q.53, I.89, E.91, G.92, C.93, L.94, S.95, I.131, C.132, H.135, E.136, H.139 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.47 Hydrogen bonds: A:Q.53, A:L.94, A:E.136, A:E.136 pi-Stacking: A:H.135

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: I.11, P.12, D.13, E.14, L.16, R.17, L.144, M.146, R.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.13, A:R.17, A:R.17, A:R.158

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 2 residues within 4Å: Chain A: R.116, D.117 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.116 Salt bridges: A:D.117 DMS.5: 4 residues within 4Å: Chain A: Q.155, R.158, Q.159, E.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirschner, H. et al., Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase. J.Med.Chem. (2024)

Release Date

2024-04-17

Peptides

Peptide deformylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide deformylase

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