SMTL ID : 9b2o.1 (1 other biounit)

Structure of the quorum quenching lactonase GcL bound to the hydrolysis product of N-octanoyl-L-homoserine lactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x 01: N-octanoyl-L-homoserine

01.1: 18 residues within 4Å: Chain A: M.36, W.40, F.62, F.101, H.132, H.134, L.135, D.136, H.137, G.170, A.171, H.212, D.234, Y.237, I.251, H.280 Ligands: CO.2, FE.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.40, A:F.101, A:A.171, A:I.251 Hydrogen bonds: A:D.234, A:Y.237 Salt bridges: A:H.132, A:H.134, A:H.212 01.6: 17 residues within 4Å: Chain B: M.36, W.40, F.62, M.100, F.101, H.132, H.134, L.135, D.136, H.137, A.171, H.212, D.234, Y.237, H.280 Ligands: CO.7, FE.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.40, B:F.101, B:A.171 Hydrogen bonds: B:Y.237 Salt bridges: B:H.132, B:H.134, B:H.212

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

CO.2: 6 residues within 4Å: Chain A: H.132, H.134, H.212, D.234 Ligands: 01.1, FE.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.132, A:H.134, A:H.212, A:D.234, 01.1 CO.7: 6 residues within 4Å: Chain B: H.132, H.134, H.212, D.234 Ligands: 01.6, FE.8 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.132, B:H.134, B:H.212, B:D.234

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

SO4.3: 5 residues within 4Å: Chain A: N.196, L.206, R.264, R.267, I.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.196 Salt bridges: A:R.264, A:R.267 SO4.4: 2 residues within 4Å: Chain A: E.194, D.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.195 SO4.9: 4 residues within 4Å: Chain B: N.196, R.264, R.267, I.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.196 Salt bridges: B:R.264, B:R.267 SO4.10: 2 residues within 4Å: Chain B: E.194, D.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.195

2 x FE: FE (III) ION(Non-covalent)

FE.5: 6 residues within 4Å: Chain A: D.136, H.137, D.234, H.280 Ligands: 01.1, CO.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.136, A:H.137, A:D.234, A:D.234, A:H.280 FE.8: 6 residues within 4Å: Chain B: D.136, H.137, D.234, H.280 Ligands: 01.6, CO.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.136, B:H.137, B:D.234, B:H.280, 01.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Corbella, M. et al., Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. Jacs Au (2024)

Release Date

2024-11-06

Peptides

GcL lactonase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
F

GcL lactonase

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