SMTL ID : 6zrg.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

1 x QP2: (4R,5S)-3-{[(3S,5S)-5-({[amino(dihydroxy)methyl]amino}methyl)pyrrolidin-3-yl]sulfanyl}-5-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid(Non-covalent)

QP2.1: 14 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, E.222, L.225, P.226, R.228 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.83, A:V.98, A:Y.189, A:L.225 Hydrogen bonds: A:S.48, A:S.48, A:S.96, A:L.225, A:R.228 Water bridges: A:S.48, A:S.48, A:K.186, A:K.186 Salt bridges: A:K.186, A:R.228

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

EDO.2: 3 residues within 4Å: Chain A: R.106, I.131, D.132 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.132 EDO.3: 1 residues within 4Å: Chain A: R.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.141 Water bridges: A:E.43 EDO.4: 4 residues within 4Å: Chain A: T.88, R.90 Chain B: E.205, E.207 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Water bridges: B:K.206, A:L.89 Hydrogen bonds: A:T.88, A:T.88, A:R.90, A:R.90 EDO.5: 2 residues within 4Å: Chain A: S.121, Q.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.121, A:Q.125 EDO.6: 6 residues within 4Å: Chain A: Y.181, V.183, T.233, 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.176, A:E.176 EDO.7: 2 residues within 4Å: Chain A: R.106 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.106 Water bridges: A:R.106

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

SO4.8: 3 residues within 4Å: Chain A: R.78, P.99 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.78, A:R.78, A:Q.103 Salt bridges: A:R.78 SO4.10: 3 residues within 4Å: Chain B: N.19, R.39, K.42 9 PLIP interactions: 9 interactions with chain B Water bridges: B:G.20, B:D.36, B:R.39, B:R.39, B:K.42, B:K.42, B:K.42 Salt bridges: B:R.39, B:K.42

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

CL.9: 2 residues within 4Å: Chain A: Q.102, R.192 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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