SMTL ID : 6cgy.1

Structure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound to a phosphate anion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: K.211, E.260, R.272, F.273, Y.281 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.211, A:E.260, A:R.272, A:R.272, A:Y.281 GOL.6: 5 residues within 4Å: Chain B: K.211, E.260, R.272, F.273, Y.281 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.211, B:E.260, B:R.272, B:R.272, B:Y.281

6 x CO: COBALT (II) ION(Non-covalent)

CO.2: 6 residues within 4Å: Chain A: D.121, H.122, D.219, H.265 Ligands: CO.3, PO4.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.121, A:H.122, A:D.219, A:D.219, A:H.265 CO.3: 6 residues within 4Å: Chain A: H.117, H.119, H.197, D.219 Ligands: CO.2, PO4.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.117, A:H.119, A:H.197, A:D.219 CO.7: 6 residues within 4Å: Chain B: D.121, H.122, D.219, H.265 Ligands: CO.8, PO4.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.121, B:H.122, B:D.219, B:D.219, B:H.265 CO.8: 6 residues within 4Å: Chain B: H.117, H.119, H.197, D.219 Ligands: CO.7, PO4.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.117, B:H.119, B:H.197, B:D.219 CO.12: 6 residues within 4Å: Chain C: D.121, H.122, D.219, H.265 Ligands: CO.13, PO4.15 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.121, C:H.122, C:D.219, C:D.219, C:H.265 CO.13: 6 residues within 4Å: Chain C: H.117, H.119, H.197, D.219 Ligands: CO.12, PO4.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.117, C:H.119, C:H.197, C:D.219

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

EDO.4: 5 residues within 4Å: Chain A: S.259, E.260, V.261, F.263, Q.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.259, A:V.261, A:Q.269 EDO.9: 6 residues within 4Å: Chain B: Y.148, D.163, I.166, K.167 Chain C: Y.148, W.159 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.163, B:K.167 EDO.10: 3 residues within 4Å: Chain B: R.177, N.192, F.193 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.177 Water bridges: B:N.192, B:F.193 EDO.14: 5 residues within 4Å: Chain C: K.211, E.260, R.272, F.273, Y.281 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.211, C:K.211, C:R.272, C:Y.281

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 11 residues within 4Å: Chain A: H.117, H.119, L.120, D.121, H.122, H.197, D.219, Y.222, H.265 Ligands: CO.2, CO.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.121 Salt bridges: A:H.119, A:H.122, A:H.197, A:H.265 PO4.11: 11 residues within 4Å: Chain B: H.117, H.119, L.120, D.121, H.122, H.197, D.219, Y.222, H.265 Ligands: CO.7, CO.8 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:H.119, B:H.122, B:H.197, B:H.265 PO4.15: 11 residues within 4Å: Chain C: H.117, H.119, L.120, D.121, H.122, H.197, D.219, Y.222, H.265 Ligands: CO.12, CO.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.222 Salt bridges: C:H.119, C:H.122, C:H.197, C:H.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bergonzi, C. et al., Structural and Biochemical Characterization of AaL, a Quorum Quenching Lactonase with Unusual Kinetic Properties. Sci Rep (2018)

Release Date

2018-08-15

Peptides

Beta-lactamase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Beta-lactamase

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