SMTL ID : 9b2j.1 (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

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

SO4.1: 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 SO4.3: 4 residues within 4Å: Chain A: N.196, 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: R.264, R.267 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.267, A:R.267 Salt bridges: A:R.267 SO4.5: 4 residues within 4Å: Chain A: W.187, R.188, T.189, K.191 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.189, A:T.189 Water bridges: A:K.191, A:K.191 Salt bridges: A:K.191 SO4.11: 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 SO4.12: 1 residues within 4Å: Chain B: R.289 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.289 SO4.14: 1 residues within 4Å: Chain B: R.165 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.165 Salt bridges: B:R.165

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.9 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.3 CO.13: 5 residues within 4Å: Chain B: H.132, H.134, H.212, D.234 Ligands: FE.19 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.10

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

ACT.6: 4 residues within 4Å: Chain A: N.46, N.52, A.55, Q.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.46, A:N.52, A:N.52, A:Q.56 ACT.15: 3 residues within 4Å: Chain B: N.83, N.85, R.92 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.85 Hydrogen bonds: B:N.85 Salt bridges: B:R.92

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

EDO.7: 2 residues within 4Å: Chain A: N.85, R.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85, A:R.92 EDO.8: 5 residues within 4Å: Chain A: E.108, N.113, R.114, Q.117, T.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.113, A:R.114 EDO.10: 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 EDO.16: 3 residues within 4Å: Chain B: K.38, H.45, E.58 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.38, B:E.58 EDO.17: 5 residues within 4Å: Chain B: G.158, Q.161, C.162, Q.167, W.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.167, B:Q.167 Water bridges: B:Q.161 EDO.18: 5 residues within 4Å: Chain B: W.40, F.101, G.170, A.171, M.251 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.171

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

FE.9: 5 residues within 4Å: Chain A: D.136, H.137, D.234, H.280 Ligands: CO.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.136, A:H.137, A:D.234, A:H.280, H2O.6 FE.19: 5 residues within 4Å: Chain B: D.136, H.137, D.234, H.280 Ligands: CO.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.136, B:H.137, B:D.234, B:H.280, H2O.14

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
A

B
C

quorum-quenching N-acyl-homoserine lactonase

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