SMTL ID : 6cgz.1 (1 other biounit)

Structure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound to C6-AHL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 6 residues within 4Å: Chain A: D.121, H.122, D.219, H.265 Ligands: CO.2, HL6.7 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.2: 6 residues within 4Å: Chain A: H.117, H.119, H.197, D.219 Ligands: CO.1, HL6.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.117, A:H.119, A:H.197, A:D.219 CO.10: 6 residues within 4Å: Chain B: D.121, H.122, D.219, H.265 Ligands: CO.11, HL6.14 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.121, B:H.122, B:D.219, B:H.265, H2O.9 CO.11: 6 residues within 4Å: Chain B: H.117, H.119, H.197, D.219 Ligands: CO.10, HL6.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.117, B:H.119, B:H.197, B:D.219

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

EDO.3: 4 residues within 4Å: Chain A: E.260, V.261, F.263, Q.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.261 EDO.4: 2 residues within 4Å: Chain A: E.138, R.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.177, A:R.177 EDO.5: 4 residues within 4Å: Chain A: N.151, Q.152, T.153, W.159 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: R.177, D.178, E.179, N.192 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.178, B:N.192 Water bridges: B:D.180, B:D.180, B:N.192 EDO.13: 4 residues within 4Å: Chain B: D.139, G.143, Q.146, W.199 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: D.139, S.142, G.143, Q.146, W.199 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.143, A:Q.146 Water bridges: A:Q.146, A:Q.146, A:Q.146

2 x HL6: N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide(Non-covalent)

HL6.7: 12 residues within 4Å: Chain A: F.47, H.117, H.119, L.120, D.121, A.156, H.197, D.219, Y.222, H.265 Ligands: CO.1, CO.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.156 Hydrogen bonds: A:Y.222 Salt bridges: A:H.117, A:H.119, A:H.122, A:H.197, A:H.265 HL6.14: 14 residues within 4Å: Chain B: M.21, W.25, F.47, F.86, H.119, L.120, D.121, A.156, H.197, D.219, Y.222, H.265 Ligands: CO.10, CO.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.25, B:F.86, B:A.156 Hydrogen bonds: B:Y.222 Salt bridges: B:H.117, B:H.119, B:H.122, B:H.197, B:H.265

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 5 residues within 4Å: Chain A: N.181, V.183, K.189, H.205, T.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.189 Water bridges: A:H.205 PG4.9: 7 residues within 4Å: Chain A: R.177, D.178, E.179, D.180, N.192, F.193, R.245 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.192 PG4.15: 5 residues within 4Å: Chain B: N.181, V.183, K.189, H.205, T.257 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.189 Water bridges: B:H.205

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase

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