SMTL ID : 7r6z.1

OXA-48 bound by Compound 3.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 3I0: 4-amino-5-hydroxynaphthalene-2,7-disulfonic acid(Non-covalent)

3I0.1: 13 residues within 4Å: Chain A: S.49, I.81, W.84, S.97, V.99, K.187, T.188, G.189, Y.190, S.223, R.229 Ligands: DMS.3, EDO.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.81, A:Y.190, A:Y.190 Hydrogen bonds: A:S.49, A:S.49, A:S.97, A:T.188, A:S.223 Water bridges: A:S.97 Salt bridges: A:K.187, A:R.229 3I0.7: 12 residues within 4Å: Chain B: S.49, I.81, W.84, S.97, V.99, K.187, T.188, G.189, Y.190, R.229 Ligands: DMS.9, EDO.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.81, B:Y.190 Hydrogen bonds: B:S.49, B:S.49, B:S.97, B:T.188 Water bridges: B:S.97 Salt bridges: B:K.187, B:R.229 pi-Stacking: B:Y.190

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: R.153, H.157, K.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.153, A:R.153 EDO.4: 4 residues within 4Å: Chain A: I.81, T.83, Y.96 Ligands: 3I0.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.83, A:T.83 Water bridges: A:T.83 EDO.8: 2 residues within 4Å: Chain B: A.112, R.113 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain B: Y.190, S.191, T.192, R.193 Ligands: 3I0.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.190, B:T.192, B:R.193, B:R.193, B:R.193

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

DMS.3: 5 residues within 4Å: Chain A: L.137, Y.190, T.192, R.193 Ligands: 3I0.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.193 DMS.9: 3 residues within 4Å: Chain B: T.83, Y.96 Ligands: 3I0.7 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: R.185 Chain B: R.185 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: S.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, D.M. et al., Unique Diacidic Fragments Inhibit the OXA-48 Carbapenemase and Enhance the Killing of Escherichia coli Producing OXA-48. Acs Infect Dis. (2021)

Release Date

2021-12-01

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase

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