SMTL ID : 7khy.1

Crystal structure of OXA-163 K73A in complex with meropenem

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

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

MER.1: 11 residues within 4Å: Chain A: A.48, S.49, W.84, S.97, V.99, L.137, T.188, G.189, Y.190, L.222, R.225 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.99, A:L.137, A:Y.190 Hydrogen bonds: A:S.49, A:S.97, A:T.188, A:G.189, A:Y.190 Salt bridges: A:K.187, A:R.225 MER.7: 11 residues within 4Å: Chain B: A.48, S.49, W.84, S.97, V.99, L.137, T.188, G.189, Y.190, L.222, R.225 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.99, B:L.137, B:Y.190 Hydrogen bonds: B:S.49, B:S.97, B:T.188, B:G.189, B:Y.190 Salt bridges: B:K.187, B:R.225

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 5 residues within 4Å: Chain A: W.4, W.26, I.149, S.150, R.153 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.4, A:W.26, A:W.26, A:I.149 Hydrogen bonds: A:R.153 Water bridges: A:S.150, A:S.150 MPD.8: 5 residues within 4Å: Chain B: W.4, W.26, I.149, S.150, R.153 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.4, B:W.26, B:W.26, B:I.149 Hydrogen bonds: B:R.153 Water bridges: B:S.150, B:S.150

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

CL.3: 4 residues within 4Å: Chain A: S.49, V.99, Y.102, W.136 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.185 Chain B: R.185 Ligands: CL.10 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: S.49, V.99, Y.102, W.136 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.185 Chain B: R.185 Ligands: CL.4 Ligand excluded by PLIP

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: E.16, H.17, E.231 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.17, A:E.231, A:E.231 ZN.6: 1 residues within 4Å: Chain A: H.161 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.161, H2O.6 ZN.11: 3 residues within 4Å: Chain B: E.16, H.17, E.231 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.17, B:E.231, B:E.231 ZN.12: 1 residues within 4Å: Chain B: H.161 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.161, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stojanoski, V. et al., Mechanistic Basis of OXA-48-like beta-Lactamases' Hydrolysis of Carbapenems. Acs Infect Dis. (2021)

Release Date

2021-02-10

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-lactamase

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