SMTL ID : 6zrj.1 (3 other biounits)

Crystal structure of class D Beta-lactamase OXA-48 in complex with ertapenem

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 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: 15 residues within 4Å: Chain A: A.69, S.70, K.73, I.102, T.104, W.105, Y.117, S.118, V.120, L.158, T.209, G.210, Y.211, L.247, R.250 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.120, A:L.158, A:Y.211 Hydrogen bonds: A:S.70, A:S.118, A:T.209, A:T.209, A:Y.211 Water bridges: A:R.250, A:R.250 Salt bridges: A:R.250 2RG.5: 13 residues within 4Å: Chain B: A.69, S.70, I.102, T.104, W.105, Y.117, S.118, V.120, L.158, G.210, Y.211, L.247, R.250 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.120, B:L.158, B:Y.211 Hydrogen bonds: B:S.70, B:T.104, B:T.209, B:Y.211 Water bridges: B:T.209, B:R.250 Salt bridges: B:R.250

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

EDO.2: 5 residues within 4Å: Chain A: L.81, D.82, S.184, R.186, S.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.184, A:R.186, A:S.187 Water bridges: A:R.186 EDO.3: 7 residues within 4Å: Chain A: D.229, D.230 Chain B: V.92, D.108, H.109, N.110, T.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.229 EDO.6: 9 residues within 4Å: Chain A: K.116 Chain B: N.200, G.201, D.202, Y.203, I.204, E.227, L.228, D.229 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.200, B:L.228, B:D.229 EDO.7: 8 residues within 4Å: Chain B: K.39, S.40, M.239, D.240, M.241, P.242, G.246, L.249 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.39 EDO.8: 5 residues within 4Å: Chain B: L.81, D.82, S.184, R.186, S.187 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.82, B:S.184, B:R.186 EDO.9: 4 residues within 4Å: Chain A: V.92, H.109, N.110 Chain B: D.229 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.229 EDO.10: 4 residues within 4Å: Chain B: Q.64, A.65, F.66, P.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.64 Water bridges: B:Q.64, B:E.216 EDO.11: 4 residues within 4Å: Chain A: H.90, Q.193 Chain B: Y.177, E.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.193 Water bridges: A:H.90, A:Q.193

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

CL.4: 2 residues within 4Å: Chain A: R.206 Chain B: R.206 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

2021-07-21

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase

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