SMTL ID : 6n9i.2 (1 other biounit)

Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus - free

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 5 residues within 4Å: Chain A: H.132, H.134, H.212, D.234 Ligands: FE.18 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.6 CO.20: 5 residues within 4Å: Chain B: H.132, H.134, H.212, D.234 Ligands: FE.37 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.15

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

SO4.2: 5 residues within 4Å: Chain A: N.196, R.264, R.267, I.268 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.196 Water bridges: A:R.267 Salt bridges: A:R.264, A:R.267 SO4.3: 4 residues within 4Å: Chain A: W.187, R.188, T.189, K.191 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.187, A:T.189 Water bridges: A:K.191, A:K.191, A:K.191, A:K.191 Salt bridges: A:K.191 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 SO4.5: 2 residues within 4Å: Chain A: R.264, R.267 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.263, A:R.267 Salt bridges: A:R.267 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.46, A:N.52, A:Q.56, A:Q.56 Water bridges: A:Q.56, A:Q.56 SO4.21: 5 residues within 4Å: Chain B: N.196, R.264, R.267, I.268 Ligands: GOL.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.196 Water bridges: B:E.271 Salt bridges: B:R.264, B:R.267 SO4.22: 4 residues within 4Å: Chain B: W.187, R.188, T.189, K.191 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.187, B:T.189 Water bridges: B:K.191, B:K.191, B:K.191, B:K.191 Salt bridges: B:K.191 SO4.23: 2 residues within 4Å: Chain B: E.194, D.195 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.195 Water bridges: B:E.194 SO4.24: 2 residues within 4Å: Chain B: R.264, R.267 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.263, B:R.267 Salt bridges: B:R.267 SO4.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.27: 4 residues within 4Å: Chain B: N.46, N.52, A.55, Q.56 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.46, B:N.52, B:Q.56, B:Q.56 Water bridges: B:Q.56, B:Q.56

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: N.196, K.204, H.220, I.268, T.272 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.196, A:K.204, A:H.220 Water bridges: A:K.204 GOL.28: 6 residues within 4Å: Chain B: N.196, K.204, H.220, I.268, T.272 Ligands: SO4.21 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.196, B:K.204, B:H.220 Water bridges: B:K.204

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

ACT.10: 5 residues within 4Å: Chain A: R.192, S.210, Y.253, D.254 Chain B: L.256 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.210, A:Y.253, A:Y.253 Salt bridges: A:R.192 Hydrophobic interactions: B:L.256 ACT.11: 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.29: 5 residues within 4Å: Chain A: L.256 Chain B: R.192, S.210, Y.253, D.254 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.210, B:Y.253 Salt bridges: B:R.192 Hydrophobic interactions: A:L.256 ACT.30: 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

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

EDO.12: 2 residues within 4Å: Chain A: Y.127, R.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.188 Water bridges: A:Y.127 EDO.13: 3 residues within 4Å: Chain A: Y.172, A.213, W.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.214 EDO.14: 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.15: 1 residues within 4Å: Chain A: I.251 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.171, A:I.252 EDO.16: 3 residues within 4Å: Chain A: Q.275, K.287, Y.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.275, A:K.287 EDO.17: 4 residues within 4Å: Chain A: N.166, Q.167, K.168, E.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.166, A:K.168, A:E.169, A:E.169 EDO.31: 2 residues within 4Å: Chain B: Y.127, R.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.188 Water bridges: B:Y.127, B:Y.127 EDO.32: 3 residues within 4Å: Chain B: Y.172, A.213, W.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.172, B:W.214 EDO.33: 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.34: 1 residues within 4Å: Chain B: I.251 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.171, B:I.252 EDO.35: 3 residues within 4Å: Chain B: Q.275, K.287, Y.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.275, B:K.287, B:Y.296 EDO.36: 4 residues within 4Å: Chain B: N.166, Q.167, K.168, E.169 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.166, B:K.168, B:E.169, B:E.169

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

FE.18: 5 residues within 4Å: Chain A: D.136, H.137, D.234, H.280 Ligands: CO.1 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.136, A:H.137, A:D.234, A:H.280, H2O.2, H2O.5 FE.37: 5 residues within 4Å: Chain B: D.136, H.137, D.234, H.280 Ligands: CO.20 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.136, B:H.137, B:D.234, B:H.280, H2O.11, H2O.15

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

PGE.19: 6 residues within 4Å: Chain A: K.25, Y.27, Q.117, L.118, K.119, Y.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.27 PGE.38: 6 residues within 4Å: Chain B: K.25, Y.27, Q.117, L.118, K.119, Y.295 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Putative hydrolase

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