SMTL ID : 7k5v.1

OXA-48 bound by Compound 3.1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x BIH: NAPHTHALENE-2,6-DISULFONIC ACID(Non-covalent)

BIH.1: 10 residues within 4Å: Chain A: S.49, S.97, V.99, K.187, T.188, G.189, Y.190, T.192, R.193, R.229 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.99, A:Y.190, A:Y.190 Hydrogen bonds: A:S.97, A:T.188, A:T.192 Salt bridges: A:K.187, A:R.193, A:R.229 BIH.5: 9 residues within 4Å: Chain B: S.49, S.97, V.99, T.188, G.189, Y.190, T.192, R.193, R.229 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.99, B:Y.190, B:Y.190 Hydrogen bonds: B:S.97, B:T.188 Salt bridges: B:R.193, B:R.229 pi-Stacking: B:W.84

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

CL.2: 3 residues within 4Å: Chain A: Q.172, R.185 Chain B: R.185 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: I.91, K.95, A.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.91, A:K.95 NA.4: 6 residues within 4Å: Chain A: L.46, L.137, S.191, T.192, R.193, I.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.191, A:T.192, A:R.193, A:I.194 NA.7: 4 residues within 4Å: Chain B: L.60, V.65, K.66, R.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.65, B:R.165 NA.8: 4 residues within 4Å: Chain B: L.46, S.191, I.194, P.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.191, B:I.194

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

EDO.6: 5 residues within 4Å: Chain B: I.109, G.110, E.111, A.112, R.113 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.111, B:E.111, B:A.112, B:R.113, B:R.113

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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