SMTL ID : 6n9i.1 (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.13 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.16: 5 residues within 4Å: Chain B: H.132, H.134, H.212, D.234 Ligands: FE.28 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.13

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

SO4.2: 4 residues within 4Å: Chain A: N.196, R.264, R.267, I.268 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: 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 SO4.4: 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 SO4.17: 1 residues within 4Å: Chain B: R.165 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.165

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

ACT.5: 4 residues within 4Å: Chain A: R.23, K.25, D.70, P.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.70 ACT.6: 4 residues within 4Å: Chain A: N.46, N.52, A.55, Q.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.46 ACT.19: 2 residues within 4Å: Chain B: N.85, R.92 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.85, B:R.92 Salt bridges: B:R.92 ACT.20: 4 residues within 4Å: Chain B: Q.275, V.276, F.278, Q.284 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.278 Hydrogen bonds: B:V.276

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

EDO.7: 4 residues within 4Å: Chain A: S.210, Y.253, D.254 Chain B: L.256 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.210, A:Y.253, A:D.254 Water bridges: A:R.192, A:S.210, A:S.210, A:Y.253 EDO.8: 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.9: 3 residues within 4Å: Chain A: R.188, I.197, L.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.188 EDO.10: 1 residues within 4Å: Chain A: I.251 4 PLIP interactions: 4 interactions with chain A Water bridges: A:A.171, A:I.252, A:I.252, A:I.252 EDO.11: 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.12: 5 residues within 4Å: Chain A: E.108, N.113, R.114, Q.117, T.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.113, A:R.114 Water bridges: A:S.291, A:S.291 EDO.21: 3 residues within 4Å: Chain B: N.196, K.204, I.268 No protein-ligand interaction detected (PLIP) EDO.22: 4 residues within 4Å: Chain B: Y.127, T.148, R.188, I.197 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.188, B:R.188 EDO.23: 3 residues within 4Å: Chain B: K.38, H.45, E.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.38, B:H.45, B:E.58 EDO.24: 6 residues within 4Å: Chain B: G.158, Q.161, C.162, R.165, Q.167, W.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.167, B:Q.167 Water bridges: B:W.214 EDO.25: 1 residues within 4Å: Chain B: I.251 No protein-ligand interaction detected (PLIP) EDO.26: 4 residues within 4Å: Chain B: Q.275, K.287, F.288, Y.296 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.275, B:K.287 Water bridges: B:Q.284 EDO.27: 4 residues within 4Å: Chain A: L.256 Chain B: R.192, S.210, Y.253 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.210, B:Y.253 Water bridges: B:R.192, B:S.210

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

FE.13: 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.1, H2O.5 FE.28: 5 residues within 4Å: Chain B: D.136, H.137, D.234, H.280 Ligands: CO.16 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.8, H2O.14

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

PGE.14: 8 residues within 4Å: Chain A: H.134, Y.172, H.212, A.213, W.214, I.251, Y.253 Ligands: PGE.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.214 Water bridges: A:I.252, A:I.252 PGE.15: 7 residues within 4Å: Chain A: G.158, Q.161, C.162, R.165, Q.167, W.214 Ligands: PGE.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.167 Water bridges: A:G.158 PGE.29: 4 residues within 4Å: Chain B: K.25, Y.27, L.118, Y.295 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.295 Water bridges: B:Y.27

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 5 residues within 4Å: Chain B: H.134, Y.172, A.213, W.214, Y.253 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.172, B:W.214 Water bridges: B:H.134, B:H.134

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
A

B
C

Putative hydrolase

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