SMTL ID : 6n9q.1

Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bind to substrate C4-AHL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 6 residues within 4Å: Chain A: H.117, H.119, H.197, D.219 Ligands: HL4.5, FE.16 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.117, A:H.119, A:H.197, A:D.219, H2O.1 CO.21: 6 residues within 4Å: Chain B: H.117, H.119, H.197, D.219 Ligands: HL4.24, FE.34 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.117, B:H.119, B:H.197, B:D.219, H2O.4

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

SO4.2: 5 residues within 4Å: Chain A: N.181, R.249, R.252, I.253 Ligands: PGE.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.181 Salt bridges: A:R.249, A:R.252 SO4.3: 2 residues within 4Å: Chain A: R.177, H.178 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.177 Salt bridges: A:R.177, A:H.178 SO4.4: 5 residues within 4Å: Chain A: E.108, D.109, I.110, R.111, N.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.131 Water bridges: A:R.111 SO4.22: 5 residues within 4Å: Chain B: N.181, R.249, R.252, I.253 Ligands: PGE.36 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.249, B:R.252 SO4.23: 5 residues within 4Å: Chain B: E.108, D.109, I.110, R.111, N.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.109, B:N.131

2 x HL4: N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide(Non-covalent)

HL4.5: 14 residues within 4Å: Chain A: M.19, M.21, F.47, F.86, H.119, D.121, A.156, H.197, D.219, Y.222, H.265 Ligands: CO.1, EDO.11, FE.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.47, A:F.86 Hydrogen bonds: A:Y.222 Salt bridges: A:H.119, A:H.197, A:H.265 HL4.24: 15 residues within 4Å: Chain B: M.19, M.21, W.25, F.47, F.86, H.119, D.121, A.156, H.197, D.219, Y.222, H.265 Ligands: CO.21, EDO.27, FE.34 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.25, B:F.47, B:F.86 Hydrogen bonds: B:Y.222 Salt bridges: B:H.119, B:H.197, B:H.265

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

EDO.6: 4 residues within 4Å: Chain A: Q.260, V.261, F.263, Q.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.261, A:Q.269 EDO.7: 4 residues within 4Å: Chain A: T.130, N.131, T.133, Q.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.130 Water bridges: A:T.133, A:T.133 EDO.8: 2 residues within 4Å: Chain A: E.138, N.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.138, A:N.142, A:N.142 EDO.9: 3 residues within 4Å: Chain A: P.209, E.210, G.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.209 EDO.10: 4 residues within 4Å: Chain A: A.254, Q.255, K.258, S.259 No protein-ligand interaction detected (PLIP) EDO.11: 1 residues within 4Å: Ligands: HL4.5 No protein-ligand interaction detected (PLIP) EDO.12: 6 residues within 4Å: Chain A: P.69, S.71, M.72, W.88, A.90, Y.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.68, A:S.71, A:M.72, A:W.88, A:A.90 EDO.13: 4 residues within 4Å: Chain A: H.119, Y.157, A.198, W.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.157, A:W.199, A:W.199 EDO.25: 5 residues within 4Å: Chain B: Q.260, V.261, F.263, Q.269 Ligands: EDO.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.261 EDO.26: 5 residues within 4Å: Chain B: T.130, N.131, A.132, T.133, Q.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.133, B:T.133 EDO.27: 1 residues within 4Å: Ligands: HL4.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.156 EDO.28: 4 residues within 4Å: Chain B: P.209, E.210, T.211, G.212 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.213 EDO.29: 4 residues within 4Å: Chain B: Q.260, W.262, Q.269 Ligands: EDO.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.260, B:Q.269 EDO.30: 5 residues within 4Å: Chain B: P.69, S.71, M.72, W.88, Y.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.68, B:S.71, B:M.72 EDO.31: 4 residues within 4Å: Chain B: W.172, R.173, T.174, K.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.172, B:T.174, B:K.176

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

1PE.14: 3 residues within 4Å: Chain A: Q.102, L.103, K.104 No protein-ligand interaction detected (PLIP) 1PE.15: 5 residues within 4Å: Chain A: Y.112, R.173, I.182, L.183, L.184 No protein-ligand interaction detected (PLIP) 1PE.32: 7 residues within 4Å: Chain B: K.10, Y.12, D.55, Q.102, K.104, Y.280 Ligands: 1PE.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.12, B:D.55 1PE.33: 8 residues within 4Å: Chain B: D.55, H.56, P.57, G.59, K.60, K.104, D.109 Ligands: 1PE.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.55, B:K.60

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

FE.16: 6 residues within 4Å: Chain A: D.121, H.122, D.219, H.265 Ligands: CO.1, HL4.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.121, A:H.122, A:D.219, A:H.265, H2O.1 FE.34: 6 residues within 4Å: Chain B: D.121, H.122, D.219, H.265 Ligands: CO.21, HL4.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.121, B:H.122, B:D.219, B:H.265, H2O.4

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

ACT.17: 4 residues within 4Å: Chain A: W.172, R.173, T.174, K.176 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.176 ACT.18: 2 residues within 4Å: Chain A: R.18, K.271 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.18 ACT.35: 2 residues within 4Å: Chain B: R.18, K.271 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.18, B:K.271

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

PGE.19: 7 residues within 4Å: Chain A: G.187, V.188, K.189, L.191, H.205, E.207 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.189 PGE.20: 10 residues within 4Å: Chain A: P.233, P.234, G.235, I.236, I.237 Chain B: P.233, P.234, G.235, I.236, I.237 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.237, B:I.237 PGE.36: 6 residues within 4Å: Chain B: N.181, K.189, L.191, H.205, I.253 Ligands: SO4.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.181, B:K.189 PGE.37: 3 residues within 4Å: Chain B: Y.112, R.173, I.182 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

Lactonase GcL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
P

Lactonase GcL