SMTL ID : 8faj.1

OXA-48-NA-1-157 inhibitor complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x Y33: (5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid(Covalent)

Y33.1: 12 residues within 4Å: Chain A: A.69, S.70, W.105, S.118, V.120, L.158, K.208, T.209, G.210, Y.211, L.247, R.250 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.105, A:L.158, A:L.247 Hydrogen bonds: A:S.70, A:S.118, A:S.118, A:T.209, A:Y.211, A:R.250 Water bridges: A:K.208 Salt bridges: A:K.208, A:R.250 Y33.7: 11 residues within 4Å: Chain B: A.69, S.70, W.105, S.118, V.120, L.158, T.209, G.210, Y.211, L.247, R.250 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.105, B:L.158, B:L.247 Hydrogen bonds: B:S.70, B:S.118, B:S.118, B:T.209, B:T.209, B:Y.211 Water bridges: B:T.213 Salt bridges: B:K.208, B:R.250

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.37, H.38, E.256 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.37, A:H.38, A:E.256, H2O.5, H2O.5 CA.3: 2 residues within 4Å: Chain A: E.89, H.90 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.89, H2O.4, H2O.8, H2O.9, H2O.11 CA.8: 2 residues within 4Å: Chain B: D.143, E.147 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.143, B:E.147, H2O.7, H2O.7, H2O.9

2 x CD: CADMIUM ION(Non-covalent)

CD.4: 1 residues within 4Å: Chain A: E.37 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.37, A:E.37, H2O.3, H2O.5, H2O.6 CD.9: 1 residues within 4Å: Chain B: D.143 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.143, B:D.143

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

CL.5: 4 residues within 4Å: Chain A: S.70, K.73, V.120, W.157 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: R.206 Chain B: R.206 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: S.70, K.73, V.120, W.157 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: K.180 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, C.A. et al., The C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Exhibits Potent Activity against Klebsiella spp. Isolates Producing OXA-48-Type Carbapenemases. Acs Infect Dis. (2023)

Release Date

2023-10-11

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase

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