SMTL ID : 6p99.1

OXA-48 carbapanemase, ertapenem complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

1RG.1: 12 residues within 4Å: Chain A: A.69, S.70, W.105, S.118, V.120, L.158, T.209, G.210, Y.211, L.247, G.248, R.250 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.120, A:L.158, A:Y.211 Hydrogen bonds: A:S.70, A:S.70, A:S.70, A:S.118, A:T.209, A:T.209, A:Y.211, A:G.248, A:R.250 Salt bridges: A:K.208, A:R.250

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

CL.2: 4 residues within 4Å: Chain A: S.70, K.73, V.120, W.157 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: R.206 Chain B: R.206 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.73, V.120, W.157 Ligand excluded by PLIP

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: D.143, E.147 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.143, A:E.147 CA.5: 4 residues within 4Å: Chain A: H.34, E.37, E.256 Ligands: CD.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.34, A:E.37, A:E.37, A:E.256, H2O.1 CA.10: 3 residues within 4Å: Chain B: H.34, E.37, E.256 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.34, B:E.37, B:E.37, B:E.256

3 x CD: CADMIUM ION(Non-covalent)

CD.6: 1 residues within 4Å: Chain A: E.147 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.147, A:E.147, H2O.2 CD.7: 4 residues within 4Å: Chain A: E.37, H.38, E.256 Ligands: CA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.37, A:H.38, A:E.256, A:E.256, H2O.1 CD.8: 2 residues within 4Å: Chain A: H.90 Chain B: H.178 No protein-ligand interaction detected (PLIP)

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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