SMTL ID : 6n9r.1

Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-AHL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-hexamer

Ligands

6 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, OHN.8 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.16: 6 residues within 4Å: Chain B: H.132, H.134, H.212, D.234 Ligands: FE.17, OHN.20 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.7 CO.30: 6 residues within 4Å: Chain C: H.132, H.134, H.212, D.234 Ligands: FE.31, OHN.37 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.132, C:H.134, C:H.212, C:D.234, H2O.13 CO.45: 6 residues within 4Å: Chain D: H.132, H.134, H.212, D.234 Ligands: FE.46, OHN.49 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.132, D:H.134, D:H.212, D:D.234, H2O.20 CO.59: 6 residues within 4Å: Chain E: H.132, H.134, H.212, D.234 Ligands: FE.60, OHN.61 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.132, E:H.134, E:H.212, E:D.234, H2O.25 CO.72: 6 residues within 4Å: Chain F: H.132, H.134, H.212, D.234 Ligands: FE.73, OHN.74 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.132, F:H.134, F:H.212, F:D.234, H2O.30

6 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, OHN.8 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.17: 6 residues within 4Å: Chain B: D.136, H.137, D.234, H.280 Ligands: CO.16, OHN.20 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.7 FE.31: 6 residues within 4Å: Chain C: D.136, H.137, D.234, H.280 Ligands: CO.30, OHN.37 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.136, C:H.137, C:D.234, C:H.280, H2O.13 FE.46: 6 residues within 4Å: Chain D: D.136, H.137, D.234, H.280 Ligands: CO.45, OHN.49 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.136, D:H.137, D:D.234, D:H.280, H2O.20 FE.60: 6 residues within 4Å: Chain E: D.136, H.137, D.234, H.280 Ligands: CO.59, OHN.61 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.136, E:H.137, E:D.234, E:H.280, H2O.25 FE.73: 6 residues within 4Å: Chain F: D.136, H.137, D.234, H.280 Ligands: CO.72, OHN.74 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.136, F:H.137, F:D.234, F:H.280, H2O.30

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

SO4.3: 4 residues within 4Å: Chain A: N.196, R.264, R.267, I.268 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.196, A:N.196 Salt bridges: A:R.264, A:R.267 SO4.4: 4 residues within 4Å: Chain F: N.196, R.264, R.267, I.268 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.264, F:R.267 SO4.5: 5 residues within 4Å: Chain A: W.187, R.188, T.189, K.191 Chain B: R.165 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.189 Salt bridges: A:K.191, B:R.165 Water bridges: B:R.165 SO4.6: 4 residues within 4Å: Chain A: R.192, H.193 Chain B: R.192, H.193 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.192, B:H.193, A:R.192, A:H.193 SO4.7: 2 residues within 4Å: Chain A: N.85, R.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.85 Salt bridges: A:R.92 SO4.18: 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 SO4.19: 5 residues within 4Å: Chain B: E.194, D.195 Chain C: R.264, R.267 Ligands: 1PE.29 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:R.267 Hydrogen bonds: B:D.195, B:D.195 SO4.32: 4 residues within 4Å: Chain C: N.196, R.264, R.267, I.268 4 PLIP interactions: 4 interactions with chain C Water bridges: C:N.196, C:N.196 Salt bridges: C:R.264, C:R.267 SO4.33: 4 residues within 4Å: Chain E: N.196, R.264, R.267, I.268 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.264, E:R.267 SO4.34: 5 residues within 4Å: Chain C: W.187, R.188, T.189, K.191 Chain D: R.165 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:R.165 Salt bridges: D:R.165, C:K.191 Hydrogen bonds: C:T.189 SO4.35: 4 residues within 4Å: Chain C: R.192, H.193 Chain D: R.192, H.193 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.192, D:H.193, C:R.192, C:H.193 SO4.36: 2 residues within 4Å: Chain C: N.85, R.92 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.85 Salt bridges: C:R.92 SO4.47: 4 residues within 4Å: Chain D: N.196, R.264, R.267, I.268 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.196 Salt bridges: D:R.264, D:R.267 SO4.48: 5 residues within 4Å: Chain A: R.264, R.267 Chain D: E.194, D.195 Ligands: 1PE.58 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Salt bridges: A:R.267 Hydrogen bonds: D:D.195, D:D.195 Water bridges: D:E.194

6 x OHN: N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE(Non-covalent)

OHN.8: 18 residues within 4Å: Chain A: M.34, M.36, W.40, F.62, M.100, F.101, H.134, D.136, G.170, A.171, H.212, D.234, Y.237, I.251, H.280 Chain C: M.44 Ligands: CO.1, FE.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.40, A:W.40, A:F.62, A:I.251 Water bridges: A:Y.237 Salt bridges: A:H.134, A:H.212, A:H.280 OHN.20: 15 residues within 4Å: Chain B: M.36, W.40, F.62, F.101, H.134, D.136, G.170, A.171, H.212, D.234, Y.237, I.251, H.280 Ligands: CO.16, FE.17 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.40, B:F.62, B:F.101 Hydrogen bonds: B:Y.237 Salt bridges: B:H.134, B:H.137, B:H.212, B:H.280 OHN.37: 18 residues within 4Å: Chain A: M.44 Chain C: M.34, M.36, W.40, F.62, M.100, F.101, H.134, D.136, G.170, A.171, H.212, D.234, Y.237, I.251, H.280 Ligands: CO.30, FE.31 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.40, C:W.40, C:F.62, C:I.251 Hydrogen bonds: C:Y.237 Salt bridges: C:H.134, C:H.212, C:H.280 OHN.49: 15 residues within 4Å: Chain D: M.36, W.40, F.62, F.101, H.134, D.136, G.170, A.171, H.212, D.234, Y.237, I.251, H.280 Ligands: CO.45, FE.46 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.40, D:F.62, D:F.101 Water bridges: D:H.134, D:H.134, D:Y.237 Salt bridges: D:H.134, D:H.137, D:H.212, D:H.280 OHN.61: 20 residues within 4Å: Chain E: M.34, M.36, W.40, F.62, M.100, F.101, H.134, L.135, D.136, Q.167, E.169, G.170, A.171, H.212, D.234, Y.237, I.251, H.280 Ligands: CO.59, FE.60 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:W.40, E:W.40, E:F.62, E:F.101, E:I.251 Salt bridges: E:H.134, E:H.212, E:H.280 OHN.74: 20 residues within 4Å: Chain F: M.34, M.36, W.40, F.62, M.100, F.101, H.134, L.135, D.136, Q.167, E.169, G.170, A.171, H.212, D.234, Y.237, I.251, H.280 Ligands: CO.72, FE.73 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:W.40, F:W.40, F:F.62, F:F.101, F:I.251 Hydrogen bonds: F:Y.237 Salt bridges: F:H.134, F:H.212, F:H.280

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

ACT.9: 4 residues within 4Å: Chain A: S.274, Q.275, V.276, F.278 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.276 Hydrogen bonds: A:V.276 ACT.21: 5 residues within 4Å: Chain A: R.165 Chain B: W.187, R.188, T.189, K.191 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.165, B:K.191 Hydrogen bonds: B:W.187 ACT.38: 4 residues within 4Å: Chain C: S.274, Q.275, V.276, F.278 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.276 Hydrogen bonds: C:V.276 ACT.50: 5 residues within 4Å: Chain C: R.165 Chain D: W.187, R.188, T.189, K.191 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:W.187 Salt bridges: D:K.191, C:R.165 ACT.62: 5 residues within 4Å: Chain E: W.187, R.188, T.189, K.191 Chain F: R.165 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.189 Salt bridges: E:K.191, F:R.165 ACT.63: 5 residues within 4Å: Chain E: Y.242, Q.275, V.276, F.278, Q.284 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Y.242, E:V.276 Hydrogen bonds: E:V.276, E:Q.284 ACT.64: 2 residues within 4Å: Chain E: H.112, R.121 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:H.112 ACT.75: 5 residues within 4Å: Chain E: R.165 Chain F: W.187, R.188, T.189, K.191 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Salt bridges: E:R.165, F:K.191 Hydrogen bonds: F:T.189 ACT.76: 5 residues within 4Å: Chain F: Y.242, Q.275, V.276, F.278, Q.284 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Y.242, F:V.276 Hydrogen bonds: F:V.276, F:Q.284 ACT.77: 2 residues within 4Å: Chain F: H.112, R.121 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:H.112

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

EDO.10: 2 residues within 4Å: Chain A: R.33, K.286 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: P.84, N.85, S.86, M.87, W.103, Y.110 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.204, H.220, I.268 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: P.224, E.225, G.227 Ligand excluded by PLIP EDO.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: E.153, K.191, R.192, H.193 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: T.145, N.146, A.147, T.148, Q.186 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: R.126, Y.127, T.148 Ligands: 1PE.29 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: R.267, Q.270 Chain E: I.197, L.198 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: P.224, E.225, T.226, G.227 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain B: P.89, Q.90 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: E.108, N.113, R.114, Q.117, T.292 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain C: R.33, K.286 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain C: P.84, N.85, S.86, M.87, W.103, Y.110 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain C: K.204, H.220, I.268 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain C: P.224, E.225, G.227 Ligand excluded by PLIP EDO.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain D: E.153, K.191, R.192, H.193 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain D: T.145, N.146, A.147, T.148, Q.186 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain D: R.126, Y.127, T.148 Ligands: 1PE.58 Ligand excluded by PLIP EDO.54: 4 residues within 4Å: Chain D: R.267, Q.270 Chain F: I.197, L.198 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain D: P.224, E.225, T.226, G.227 Ligand excluded by PLIP EDO.56: 2 residues within 4Å: Chain D: P.89, Q.90 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain D: E.108, N.113, R.114, Q.117, T.292 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain E: E.153, K.191, R.192, H.193 Ligand excluded by PLIP EDO.66: 2 residues within 4Å: Chain E: N.85, R.92 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain E: E.108, R.114, T.292 Ligand excluded by PLIP EDO.68: 5 residues within 4Å: Chain B: R.264, R.267 Chain E: H.193, E.194, D.195 Ligand excluded by PLIP EDO.69: 2 residues within 4Å: Chain E: R.33, K.286 Ligand excluded by PLIP EDO.78: 4 residues within 4Å: Chain F: E.153, K.191, R.192, H.193 Ligand excluded by PLIP EDO.79: 2 residues within 4Å: Chain F: N.85, R.92 Ligand excluded by PLIP EDO.80: 3 residues within 4Å: Chain F: E.108, R.114, T.292 Ligand excluded by PLIP EDO.81: 5 residues within 4Å: Chain D: R.264, R.267 Chain F: H.193, E.194, D.195 Ligand excluded by PLIP EDO.82: 2 residues within 4Å: Chain F: R.33, K.286 Ligand excluded by PLIP

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

1PE.15: 10 residues within 4Å: Chain A: Y.127, R.188, E.194, D.195, I.197, L.198, L.199 Chain F: E.263, R.267, Q.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.188, A:E.194, A:D.195, A:D.195 Water bridges: A:R.188 1PE.29: 10 residues within 4Å: Chain B: Y.127, R.188, I.197, L.198 Chain C: E.263, R.266, R.267, Q.270 Ligands: SO4.19, EDO.24 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.188, C:E.263, C:R.267 Water bridges: B:L.198 1PE.44: 10 residues within 4Å: Chain C: Y.127, R.188, E.194, D.195, I.197, L.198, L.199 Chain E: E.263, R.267, Q.270 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.188, C:D.195, C:D.195 Water bridges: C:R.188 1PE.58: 10 residues within 4Å: Chain A: E.263, R.266, R.267, Q.270 Chain D: Y.127, R.188, I.197, L.198 Ligands: SO4.48, EDO.53 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:E.263, A:E.263, A:R.267, D:R.188 Water bridges: D:L.198 1PE.70: 6 residues within 4Å: Chain E: K.25, Y.27, Q.117, L.118, K.119, Y.295 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.25, E:Y.27 Water bridges: E:K.25, E:D.70 1PE.83: 6 residues within 4Å: Chain F: K.25, Y.27, Q.117, L.118, K.119, Y.295 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.25 Water bridges: F:K.25, F:D.70

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.71: 11 residues within 4Å: Chain D: P.248, P.249, G.250, I.251, I.252 Chain E: P.248, P.249, G.250, I.251, I.252, S.255 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:I.252, E:I.252, E:I.252 PGE.84: 11 residues within 4Å: Chain B: P.248, P.249, G.250, I.251, I.252 Chain F: P.248, P.249, G.250, I.251, I.252, S.255 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:I.252, F:I.252, F:I.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bergonzi, C. et al., The Structural Determinants Accounting for the Broad Substrate Specificity of the Quorum Quenching Lactonase GcL. Chembiochem (2019)

Release Date

2019-04-03

Peptides

Putative hydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

B
X

C
P

D
X

E
A

F
A

Putative hydrolase

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