SMTL ID : 4rdy.1

Crystal structure of VmoLac bound to 3-oxo-C10 AHL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

CO.1: 6 residues within 4Å: Chain A: H.24, H.26, K.139, D.258 Ligands: CO.2, 3M5.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.24, A:H.26, A:D.258, H2O.13 CO.2: 7 residues within 4Å: Chain A: H.24, K.139, H.172, H.201, R.225 Ligands: CO.1, 3M5.3 4 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.172, A:H.201, 3M5.3, H2O.13 CO.13: 6 residues within 4Å: Chain B: H.24, H.26, K.139, D.258 Ligands: CO.14, 3M5.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.24, B:H.26, B:D.258, H2O.26 CO.14: 7 residues within 4Å: Chain B: H.24, K.139, H.172, H.201, R.225 Ligands: CO.13, 3M5.15 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.172, B:H.201, 3M5.15, H2O.26

2 x 3M5: 3-OXO-N-[(3S)-2-OXOTETRAHYDROFURAN-3-YL]DECANAMIDE(Non-covalent)

3M5.3: 21 residues within 4Å: Chain A: H.26, L.29, Y.99, Y.101, K.139, H.172, R.225, L.228, I.230, Y.231, D.258, C.260, I.263, W.265, Y.266, V.270, T.274, V.275, W.278 Ligands: CO.1, CO.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.29, A:L.228, A:L.228, A:I.230, A:Y.231, A:Y.266, A:V.270, A:T.274, A:V.275, A:W.278 Hydrogen bonds: A:Y.101, A:R.225 Water bridges: A:Y.101, A:R.225 Salt bridges: A:H.26, A:H.172, A:H.201, A:R.225 3M5.15: 17 residues within 4Å: Chain B: H.26, L.29, Y.99, K.139, H.172, R.225, Y.231, D.258, I.263, W.265, Y.266, V.270, V.271, T.274, W.278 Ligands: CO.13, CO.14 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.29, B:Y.231, B:Y.266, B:Y.266, B:V.270, B:V.271, B:W.278 Hydrogen bonds: B:Y.99, B:R.225 Water bridges: B:Y.101, B:R.225 Salt bridges: B:H.26, B:H.172, B:H.201, B:R.225

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: D.53, A.54, A.57, Y.259, T.279, M.280, T.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.280 Water bridges: A:A.54 GOL.5: 5 residues within 4Å: Chain A: L.147, R.156, D.182, R.185, E.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.156, A:D.182, A:R.185, A:E.189 GOL.6: 5 residues within 4Å: Chain A: T.100, Y.101, T.102, W.265 Chain B: F.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.101, A:T.102, A:T.102, A:W.265 Water bridges: A:G.73 GOL.7: 4 residues within 4Å: Chain A: L.181, R.185, K.188, E.217 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.181, A:R.185, A:R.185, A:K.188, A:K.188 GOL.8: 4 residues within 4Å: Chain A: R.111 Chain B: P.267, P.268 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.111 Water bridges: A:Y.107, A:Y.107 GOL.9: 7 residues within 4Å: Chain A: A.195, G.218, A.219, F.220, D.251, Q.252, R.311 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.219 GOL.10: 9 residues within 4Å: Chain A: L.41, Y.42, T.262, I.263, D.264, Y.266, P.268 Chain B: R.111 Ligands: SO4.12 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.111, A:Y.266 Water bridges: A:E.47, A:I.263, A:I.263 GOL.11: 4 residues within 4Å: Chain A: R.35, W.36, P.39, E.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.35, A:R.35 Water bridges: A:Y.42 GOL.16: 7 residues within 4Å: Chain B: A.195, G.218, A.219, F.220, D.251, Q.252, R.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.218 GOL.17: 5 residues within 4Å: Chain B: D.53, A.54, Y.259, T.279, M.280 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.259, B:M.280 Water bridges: B:A.54 GOL.18: 9 residues within 4Å: Chain A: R.111 Chain B: L.41, Y.42, T.262, I.263, D.264, Y.266, P.268 Ligands: GOL.8 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.41, B:Y.266, A:R.111 Water bridges: B:R.50, B:I.263, B:I.263 GOL.19: 8 residues within 4Å: Chain B: R.50, Y.259, C.260, P.261, I.263, P.268, V.271, W.278 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.50, B:Y.259, B:C.260 GOL.20: 3 residues within 4Å: Chain B: I.250, D.251, R.303 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.303, B:R.303 Water bridges: B:D.251

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

SO4.12: 5 residues within 4Å: Chain A: P.267, P.268, E.269 Chain B: R.111 Ligands: GOL.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:E.269, B:R.111 Salt bridges: B:R.111 SO4.21: 4 residues within 4Å: Chain B: V.175, T.205, D.207, F.210 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.205, B:D.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hiblot, J. et al., Crystal structure of VmoLac, a tentative quorum quenching lactonase from the extremophilic crenarchaeon Vulcanisaeta moutnovskia. Sci Rep (2015)

Release Date

2015-02-25

Peptides

Parathion hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Parathion hydrolase

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