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

Structure of the quorum quenching lactonase GcL bound to N-hexanoyl-L-homoserine lactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 6 residues within 4Å: Chain A: H.132, H.134, H.212, D.234 Ligands: FE.2, HL6.15 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.1 CO.18: 6 residues within 4Å: Chain B: H.132, H.134, H.212, D.234 Ligands: FE.19, HL6.35 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.4

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

FE.2: 6 residues within 4Å: Chain A: D.136, H.137, D.234, H.280 Ligands: CO.1, HL6.15 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.1 FE.19: 6 residues within 4Å: Chain B: D.136, H.137, D.234, H.280 Ligands: CO.18, HL6.35 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.4

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

EDO.3: 2 residues within 4Å: Chain A: I.197, L.198 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: R.192, H.193 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: T.145, N.146, A.147, Q.186 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: N.83, P.84, N.85, S.86, M.87, W.103, A.105, Y.110 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: N.196, K.204, L.206, H.220, I.268 Ligands: EDO.8, EDO.9, SO4.17 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: K.204 Ligands: EDO.7, EDO.9 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: G.202, V.203, H.220, E.222 Ligands: EDO.7, EDO.8 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: F.101 Ligands: HL6.15 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: P.224, E.225, T.226, G.227 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: R.188, I.197, L.198, L.199 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: T.145, N.146, A.147, Q.186 Ligands: ACT.33 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: E.153, N.157 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: D.154, G.158, Q.161 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: Q.275, W.277, Q.284, F.288 Ligands: ACT.30 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: Q.117, K.119 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: K.204, L.206, H.220, I.268 Ligands: SO4.36 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain B: R.33, K.286 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain B: M.100, G.170 Ligand excluded by PLIP

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

ACT.12: 4 residues within 4Å: Chain A: Q.275, V.276, F.278, Q.284 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.278 Hydrogen bonds: A:V.276, A:Q.284 ACT.13: 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:T.189, A:T.189 Salt bridges: A:K.191 ACT.14: 5 residues within 4Å: Chain A: E.123, D.124, I.125, R.126, N.146 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.126 Hydrogen bonds: A:N.146 ACT.29: 4 residues within 4Å: Chain B: W.187, R.188, T.189, K.191 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.189 Salt bridges: B:K.191 ACT.30: 5 residues within 4Å: Chain B: Q.275, V.276, F.278, Q.284 Ligands: EDO.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.276 ACT.31: 6 residues within 4Å: Chain B: N.83, P.84, S.86, M.87, W.103, Y.110 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.103 Hydrogen bonds: B:S.86, B:M.87, B:Y.110 ACT.32: 5 residues within 4Å: Chain B: E.123, D.124, I.125, R.126, N.146 No protein-ligand interaction detected (PLIP) ACT.33: 2 residues within 4Å: Chain B: T.145 Ligands: EDO.21 No protein-ligand interaction detected (PLIP) ACT.34: 5 residues within 4Å: Chain B: G.158, Q.161, C.162, R.165, W.214 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.214 Hydrogen bonds: B:G.158 Salt bridges: B:R.165

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

HL6.15: 15 residues within 4Å: Chain A: M.36, F.62, F.101, H.134, L.135, D.136, A.171, H.212, D.234, Y.237, I.251, H.280 Ligands: CO.1, FE.2, EDO.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.62, A:F.101 Hydrogen bonds: A:Y.237 Salt bridges: A:H.134, A:H.212, A:H.280 HL6.35: 15 residues within 4Å: Chain B: M.36, W.40, F.62, F.101, H.134, L.135, D.136, A.171, H.212, D.234, Y.237, I.251, H.280 Ligands: CO.18, FE.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.40, B:F.62, B:F.101 Water bridges: B:H.134 Salt bridges: B:H.134, B:H.212, B:H.280

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.16: 4 residues within 4Å: Chain A: K.25, Y.27, D.70, K.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.27

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

SO4.17: 5 residues within 4Å: Chain A: N.196, R.264, R.267, I.268 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.196 Salt bridges: A:R.264, A:R.267 SO4.36: 5 residues within 4Å: Chain B: N.196, R.264, R.267, I.268 Ligands: EDO.26 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.264, B:R.267

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
P

B
D

GcL lactonase

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