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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

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

DWZ.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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.102, A:V.120, A:L.158, A:Y.211 Hydrogen bonds: A:S.70, A:T.104, A:S.118, A:T.209, A:T.209, A:Y.211 Water bridges: A:T.104, A:R.250 Salt bridges: A:R.250 DWZ.6: 14 residues within 4Å: Chain B: A.69, S.70, I.102, T.104, W.105, Y.117, S.118, V.120, L.158, T.209, G.210, Y.211, L.247, R.250 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:V.120, B:L.158, B:Y.211 Hydrogen bonds: B:S.70, B:T.104, B:S.118, B:T.209, B:T.209, B:Y.211 Water bridges: B:T.104, B:R.250, B:R.250, B:R.250, 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:S.184 EDO.3: 2 residues within 4Å: Chain A: D.229, D.230 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.229 EDO.4: 3 residues within 4Å: Chain A: Y.177, E.227, V.232 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain B: Q.124, S.155, L.158, D.159, R.214 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.124, B:R.214, B:R.214 EDO.8: 5 residues within 4Å: Chain A: N.146 Chain B: Q.64, A.65, F.66, P.217 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.64, B:Q.64, B:R.163, A:N.146 EDO.9: 4 residues within 4Å: Chain B: V.120, Q.124, R.214 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.214 Water bridges: B:R.100, B:Q.124 EDO.10: 7 residues within 4Å: Chain B: K.39, S.40, M.239, D.240, M.241, P.242, L.249 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.39, B:S.40 EDO.11: 3 residues within 4Å: Chain B: Y.177, E.227, V.232 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.177

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

CL.5: 1 residues within 4Å: Chain A: 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
C

Beta-lactamase

Related Entries With Identical Sequence