SMTL ID : 6zrh.1 (1 other biounit)

Crystal structure of OXA-10loop24 in complex with ertapenem

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x 2RG: (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid(Covalent)

2RG.1: 11 residues within 4Å: Chain A: A.46, S.47, K.50, W.82, S.95, V.97, L.135, T.186, G.187, W.188, R.227 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.97, A:L.135, A:W.188 Hydrogen bonds: A:S.47, A:S.95, A:T.186, A:T.186, A:W.188 Salt bridges: A:R.227 2RG.3: 19 residues within 4Å: Chain A: P.178 Chain B: A.46, S.47, K.50, M.79, Q.81, W.82, R.84, Q.93, V.94, S.95, V.97, L.135, T.186, G.187, W.188, L.224, R.227 Ligands: EDO.8 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.94, B:V.97, B:L.135, B:W.188, A:P.178 Hydrogen bonds: B:S.47, B:Q.81, B:S.95, B:T.186, B:T.186, B:W.188 Water bridges: B:K.185 Salt bridges: B:R.84, B:R.227

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

EDO.2: 5 residues within 4Å: Chain A: N.65, H.67 Chain B: L.155, N.156, K.162 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.156, A:N.65, A:H.67 Water bridges: B:L.155, B:N.156, A:N.65 EDO.4: 6 residues within 4Å: Chain A: T.87, R.89 Chain B: E.179, Y.180, E.204, E.206 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.204, B:E.206, A:T.87 Water bridges: B:E.204, A:G.90 EDO.5: 5 residues within 4Å: Chain A: E.204, E.206 Chain B: T.87, R.89 Ligands: EDO.8 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.90, A:E.179 Water bridges: B:T.87, B:L.88, A:E.204, A:E.204, A:E.204 EDO.6: 2 residues within 4Å: Chain B: G.129, I.130 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.130 Water bridges: B:G.129 EDO.7: 2 residues within 4Å: Chain B: R.111, Y.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.111, B:Y.115, B:Y.115 Water bridges: B:T.60 EDO.8: 8 residues within 4Å: Chain A: P.178, E.179, E.206 Chain B: R.84, L.86, G.90 Ligands: 2RG.3, EDO.5 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.90

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

2021-07-21

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Beta-lactamase

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