SMTL ID : 6hoo.1

Crystal Structure of Rationally Designed OXA-48loop18 beta-lactamase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: Q.173, R.186 Chain B: Q.173, L.176, R.186 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.173, A:Q.173 Water bridges: B:Q.173, B:Q.173 Salt bridges: B:R.186, A:R.186 SO4.2: 3 residues within 4Å: Chain A: G.111, E.112, A.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.112, A:A.113 SO4.3: 4 residues within 4Å: Chain A: N.28, K.31, N.216, W.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.28, A:N.216 Salt bridges: A:K.31 SO4.4: 7 residues within 4Å: Chain A: V.72, D.88, H.89, N.90, T.93 Chain B: D.214, D.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.88, A:N.90 SO4.5: 7 residues within 4Å: Chain A: S.50, S.98, T.189, G.190, T.191, D.230, R.235 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.98, A:T.189, A:G.190, A:T.191 Salt bridges: A:K.188, A:R.235 SO4.10: 2 residues within 4Å: Chain B: S.164, E.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.165 Water bridges: B:R.166 SO4.11: 5 residues within 4Å: Chain A: D.215 Chain B: V.72, D.88, H.89, N.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.90, B:T.93 Water bridges: B:N.90 SO4.12: 7 residues within 4Å: Chain B: S.50, S.98, T.189, G.190, T.191, L.232, R.235 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.98, B:T.189, B:T.191 Water bridges: B:T.191, B:T.191 Salt bridges: B:K.188, B:R.235 SO4.13: 3 residues within 4Å: Chain B: G.111, E.112, A.113 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.112, B:A.113 Water bridges: B:R.114

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: K.3, W.27, T.147, S.151, R.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.3, A:T.147, A:R.154 Water bridges: A:K.3 GOL.7: 3 residues within 4Å: Chain A: S.164, E.165, R.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.165, A:R.166 Water bridges: A:E.165 GOL.8: 6 residues within 4Å: Chain A: K.74, W.75, D.76, R.80, P.101, E.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.74, A:D.76, A:R.80 GOL.9: 10 residues within 4Å: Chain A: N.180, G.181, D.182, Y.183, I.184, E.212, L.213, D.214 Chain B: I.92, K.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.180, A:I.184, A:E.212 GOL.14: 5 residues within 4Å: Chain B: K.3, T.147, I.150, S.151, R.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.154 GOL.15: 10 residues within 4Å: Chain A: I.92, K.96 Chain B: N.180, G.181, D.182, Y.183, I.184, E.212, L.213, D.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.180, B:D.182 GOL.16: 8 residues within 4Å: Chain B: M.95, K.96, A.174, M.175, L.176, T.177, A.187, K.188 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.187 Water bridges: B:K.96, B:A.174, B:L.176, B:K.188 GOL.17: 6 residues within 4Å: Chain B: K.74, W.75, D.76, R.80, P.101, E.105 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.76, B:D.76, B:R.80 GOL.18: 5 residues within 4Å: Chain B: N.28, N.30, K.31, N.216, W.218 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.28, B:K.31, B:N.216, B:W.218

1 x F: FLUORIDE ION(Non-covalent)

F.19: 1 residues within 4Å: Chain B: K.74 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dabos, L. et al., Substrate Specificity of OXA-48 after beta 5-beta 6 Loop Replacement. Acs Infect Dis. (2020)

Release Date

2019-10-09

Peptides

Beta-lactamase,OXA-48loop18,Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase,OXA-48loop18,Beta-lactamase