SMTL ID : 8tav.1

FphH, Staphylococcus aureus fluorophosphonate-binding serine hydrolases H, boronic acid-based compound N34 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

3 x ZKR: [5-(trifluoromethyl)thiophen-2-yl]boronic acid(Covalent)(Non-covalent)

ZKR.1: 13 residues within 4Å: Chain A: G.26, F.27, S.96, L.97, P.120, A.128, I.129, G.132, L.167, L.171, M.195, I.196, H.223 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.27 Hydrogen bonds: A:F.27, A:F.27 Water bridges: A:T.28 ZKR.2: 10 residues within 4Å: Chain A: P.68, F.69, F.72, F.101, K.104, E.169, A.170, T.173, I.174 Ligands: ZKR.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.173, A:T.173 pi-Stacking: A:F.69 pi-Cation interactions: A:K.104 ZKR.3: 8 residues within 4Å: Chain A: F.69, F.72, K.73, L.76, K.104, N.108, R.109 Ligands: ZKR.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.73, A:R.109 pi-Stacking: A:F.72

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: D.209, D.211 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.209, A:D.209, A:D.211, H2O.6, H2O.8 CA.5: 1 residues within 4Å: Chain A: E.149 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.149, H2O.2, H2O.3, H2O.5 CA.6: 1 residues within 4Å: Chain A: Q.85 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: D.152, D.156 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.152, A:D.152, A:D.156, H2O.3, H2O.5 CA.8: 1 residues within 4Å: Chain A: E.16 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.16, A:E.16, H2O.2, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Upadhyay, T. et al., Identification of covalent inhibitors of Staphylococcus aureus serine hydrolases important for virulence and biofilm formation. Nat Commun (2025)

Release Date

2024-07-17

Peptides

Fluorophosphonate-binding serine hydrolase H: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Fluorophosphonate-binding serine hydrolase H

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