SMTL ID : 5fdh.1

CRYSTAL STRUCTURE OF OXA-405 BETA-LACTAMASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: Q.172, L.175, R.185 Chain B: Q.172, R.185 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Water bridges: B:Q.172, B:Q.172, B:R.185, A:Q.172, A:Q.172, A:Q.172, A:R.185 Salt bridges: B:R.185, A:R.185 SO4.2: 4 residues within 4Å: Chain A: G.110, E.111, A.112 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.111, A:A.112 Water bridges: A:I.109, A:R.113 SO4.3: 2 residues within 4Å: Chain A: S.163, E.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.164 Water bridges: A:S.163, A:R.165 SO4.4: 8 residues within 4Å: Chain A: S.49, S.97, K.187, T.188, G.189, Y.190, R.225 Ligands: GOL.10 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.49, A:S.97, A:S.97, A:T.188, A:Y.190 Water bridges: A:R.225, A:R.225, A:R.225, A:R.225 Salt bridges: A:K.187, A:R.225 SO4.5: 4 residues within 4Å: Chain A: R.107, Q.108, G.110 Ligands: SO4.2 No protein-ligand interaction detected (PLIP) SO4.6: 3 residues within 4Å: Chain A: N.7, K.8, S.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.7, A:S.9 SO4.7: 3 residues within 4Å: Chain A: K.234, L.241, E.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.242 Salt bridges: A:K.234 SO4.8: 3 residues within 4Å: Chain A: N.27, K.30, N.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27, A:N.27, A:N.206 Salt bridges: A:K.30 SO4.11: 7 residues within 4Å: Chain B: S.49, S.97, K.187, T.188, G.189, Y.190, R.225 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.49, B:S.49, B:S.97, B:Y.190 Water bridges: B:S.97, B:T.188, B:T.188, B:R.225, B:R.225 Salt bridges: B:K.187, B:R.225 SO4.12: 4 residues within 4Å: Chain B: N.27, K.30, N.206, W.208 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.27, B:N.206 Salt bridges: B:K.30 SO4.13: 2 residues within 4Å: Chain B: S.163, E.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.164 Water bridges: B:V.162, B:R.165 SO4.14: 4 residues within 4Å: Chain B: E.6, N.7, K.8, S.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.6, B:K.8, B:S.9

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: L.60, S.163, R.165, S.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.163, A:R.165, A:S.166 Water bridges: A:R.165, A:S.166 GOL.10: 7 residues within 4Å: Chain A: S.49, K.52, S.97, V.99, L.137, Y.190 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.49, A:S.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oueslati, S. et al., Biochemical and Structural Characterization of OXA-405, an OXA-48 Variant with Extended-Spectrum beta-Lactamase Activity. Microorganisms (2019)

Release Date

2016-12-28

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase