SMTL ID : 6zw2.1

Crystal structure of OXA-10loop48 in complex with hydrolyzed meropenem

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: T.88, R.90 Chain B: E.205, E.207 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.90 Water bridges: A:L.89, B:P.179, B:E.180, B:E.205, B:K.206, B:E.207 EDO.3: 5 residues within 4Å: Chain A: Y.181, V.183, M.236, E.237, I.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.181, A:I.241 Water bridges: A:E.237, A:G.243 EDO.4: 2 residues within 4Å: Chain A: N.19, R.39 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.39 Water bridges: A:G.20, A:G.20, A:R.39, A:K.42 EDO.5: 6 residues within 4Å: Chain A: P.179, E.180, Y.181, E.207 Chain B: T.88, R.90 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.207, A:E.207, B:T.88, B:R.90 Water bridges: A:E.205, B:G.91 EDO.6: 2 residues within 4Å: Chain A: K.118, K.119 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain A: S.121, Q.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.121, A:Q.125 Water bridges: A:G.123 EDO.12: 3 residues within 4Å: Chain A: T.191, R.192 Ligands: 8YL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.191 EDO.13: 3 residues within 4Å: Chain B: E.43, Y.44, R.141 3 PLIP interactions: 3 interactions with chain B Water bridges: B:L.45, B:R.141, B:R.141

2 x 8YL: (2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfan yl-3-methyl-2,3-dihydro-1H-pyrrole-5-carboxylic acid(Non-covalent)

8YL.2: 12 residues within 4Å: Chain A: S.48, K.51, W.83, S.96, V.98, L.136, K.186, T.187, G.188, Y.189, R.228 Ligands: 8YL.11 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.83, A:V.98, A:Y.189 Hydrogen bonds: A:S.48, A:S.96, A:S.96, A:T.187 Water bridges: A:S.48, A:S.48, A:S.48, A:K.186, A:R.228 Salt bridges: A:K.186, A:R.228 8YL.11: 13 residues within 4Å: Chain A: S.48, K.51, S.96, L.136, K.186, T.187, G.188, Y.189, T.191, R.192, R.228 Ligands: 8YL.2, EDO.12 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.48, A:S.96, A:S.96, A:T.187, A:T.191 Water bridges: A:S.48, A:S.48, A:S.48, A:S.48, A:R.192, A:R.228, A:R.228 Salt bridges: A:K.186, A:R.228

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 2 residues within 4Å: Chain A: R.78, P.99 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.78 Salt bridges: A:R.78

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

CL.9: 2 residues within 4Å: Chain A: Q.102, R.192 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: R.106, D.132 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: S.96, T.187, R.228 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: S.162, K.163 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tassone, G. et al., Mechanistic insights into carbapenem hydrolysis by OXA-48 and the OXA10-derived hybrids OXA-10 loop24 and loop48. To Be Published

Release Date

2021-08-11

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase

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