SMTL ID : 9b2j.2 (1 other biounit)

Structure of the quorum quenching lactonase GcL I237M mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 1 residues within 4Å: Chain A: R.267 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.267 Salt bridges: A:R.267 ACT.9: 4 residues within 4Å: Chain A: Q.275, V.276, F.278, Q.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.276, A:Q.284 ACT.12: 1 residues within 4Å: Chain B: R.267 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.267 Salt bridges: B:R.267 ACT.20: 4 residues within 4Å: Chain B: Q.275, V.276, F.278, Q.284 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.276, B:Q.284

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

CO.2: 5 residues within 4Å: Chain A: H.132, H.134, H.212, D.234 Ligands: FE.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.132, A:H.134, A:H.212, A:D.234, H2O.4 CO.13: 5 residues within 4Å: Chain B: H.132, H.134, H.212, D.234 Ligands: FE.22 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.132, B:H.134, B:H.212, B:D.234, H2O.14

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

SO4.3: 4 residues within 4Å: Chain A: N.196, R.264, R.267, I.268 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.196 Water bridges: A:R.264, A:R.264 Salt bridges: A:R.264, A:R.267 SO4.4: 4 residues within 4Å: Chain A: W.187, R.188, T.189, K.191 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.187, A:T.189 Salt bridges: A:K.191 SO4.5: 2 residues within 4Å: Chain A: E.194, D.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.195 SO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.8: 4 residues within 4Å: Chain A: N.46, N.52, A.55, Q.56 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.46, A:N.52, A:Q.56, A:Q.56 Water bridges: A:Q.56 SO4.14: 4 residues within 4Å: Chain B: N.196, R.264, R.267, I.268 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.196 Water bridges: B:R.264, B:R.264 Salt bridges: B:R.264, B:R.267 SO4.15: 4 residues within 4Å: Chain B: W.187, R.188, T.189, K.191 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.187, B:T.189 Salt bridges: B:K.191 SO4.16: 2 residues within 4Å: Chain B: E.194, D.195 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.195 Water bridges: B:H.193, B:E.194, B:E.194, B:E.194 SO4.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.19: 4 residues within 4Å: Chain B: N.46, N.52, A.55, Q.56 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.46, B:N.52, B:Q.56, B:Q.56 Water bridges: B:Q.56

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

EDO.10: 2 residues within 4Å: Chain A: R.192, H.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.192, A:H.193 EDO.21: 2 residues within 4Å: Chain B: R.192, H.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.192, B:H.193

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

FE.11: 5 residues within 4Å: Chain A: D.136, H.137, D.234, H.280 Ligands: CO.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.136, A:H.137, A:H.280, H2O.1, H2O.8 FE.22: 5 residues within 4Å: Chain B: D.136, H.137, D.234, H.280 Ligands: CO.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.136, B:H.137, B:H.280, H2O.11, H2O.17

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

quorum-quenching N-acyl-homoserine lactonase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

quorum-quenching N-acyl-homoserine lactonase

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