SMTL ID : 6p9c.1

OXA-48 carbapanemase, doripenem complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 4J6: (4R,5S)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-3-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid(Covalent)(Non-covalent)

4J6.1: 9 residues within 4Å: Chain A: A.69, S.70, S.118, L.158, T.209, G.210, Y.211, L.247, R.250 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.158 Hydrogen bonds: A:S.70, A:S.118, A:T.209, A:T.209, A:Y.211 Water bridges: A:R.250 Salt bridges: A:R.250 4J6.8: 11 residues within 4Å: Chain B: A.69, S.70, S.118, L.158, K.208, T.209, G.210, Y.211, S.244, L.247, R.250 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.158 Hydrogen bonds: B:S.70, B:S.70, B:S.118, B:S.118, B:T.209, B:Y.211 Salt bridges: B:K.208, B:R.250

2 x O6P: Doripenem(Non-covalent)

O6P.2: 10 residues within 4Å: Chain A: N.48, K.51, L.228, D.229, D.230, N.231, W.233, E.261, K.262, I.263 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.228 Hydrogen bonds: A:N.48, A:K.51, A:K.51, A:D.230, A:D.230, A:D.230, A:N.231 O6P.9: 10 residues within 4Å: Chain B: N.48, K.51, L.228, D.229, D.230, N.231, W.233, E.261, K.262, I.263 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.228 Hydrogen bonds: B:N.48, B:D.230, B:D.230, B:D.230, B:N.231

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

CL.3: 4 residues within 4Å: Chain A: K.73, V.120, Y.123, W.157 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: R.206 Chain B: R.206 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: S.70, K.73, V.120, W.157 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: K.180 Ligand excluded by PLIP

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: H.34, E.37, E.256 Ligands: CD.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.34, A:E.37 CA.6: 1 residues within 4Å: Chain A: D.154 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.154 CA.12: 2 residues within 4Å: Chain B: D.143, E.147 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.143, B:E.147, B:E.147, H2O.6, H2O.6

2 x CD: CADMIUM ION(Non-covalent)

CD.7: 4 residues within 4Å: Chain A: E.37, H.38, E.256 Ligands: CA.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.37, A:H.38, A:E.256, A:E.256 CD.13: 3 residues within 4Å: Chain B: D.143, G.145, E.147 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.143, H2O.4, H2O.4, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, C.A. et al., Structural Insights into the Mechanism of Carbapenemase Activity of the OXA-48 beta-Lactamase. Antimicrob.Agents Chemother. (2019)

Release Date

2019-08-07

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase

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