SMTL ID : 2wyd.1

The quorum quenching N-acyl homoserine lactone acylase PvdQ in complex with dodecanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: K.25, D.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.25, A:D.26, A:D.26 Water bridges: A:K.25 GOL.2: 5 residues within 4Å: Chain A: W.82, L.83, Q.85, A.88, R.144 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.83, A:Q.85, A:R.144, A:R.144 Water bridges: A:W.82, B:Q.125 GOL.3: 4 residues within 4Å: Chain A: W.93, T.136, D.137, L.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.136 Water bridges: A:D.137 GOL.4: 5 residues within 4Å: Chain A: L.74, I.78 Chain B: V.119, E.120, H.121 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.120 Water bridges: A:V.160 GOL.5: 9 residues within 4Å: Chain A: E.49, S.68, A.69, R.145 Chain B: P.25, N.27, G.28, A.29, M.30 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.27, B:A.29, B:M.30, A:E.49 GOL.6: 5 residues within 4Å: Chain B: L.43, D.44, N.166, Q.167, A.168 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.44, B:D.44, B:N.166 Water bridges: B:R.62 GOL.7: 7 residues within 4Å: Chain B: F.380, A.381, L.383, D.384, G.385, A.386, W.387 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.381, B:A.386, B:W.387 GOL.8: 6 residues within 4Å: Chain B: R.149, A.238, W.239, R.241, A.248, G.249 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.149, B:R.149, B:W.239, B:A.248 Water bridges: B:W.239, B:R.241

2 x DAO: LAURIC ACID(Non-covalent)

DAO.9: 16 residues within 4Å: Chain A: T.143, L.146 Chain B: S.1, P.22, H.23, F.24, F.32, L.50, L.53, N.57, H.68, T.69, V.70, V.158, W.162, V.187 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.24, B:F.24, B:F.32, B:L.50, B:L.53, B:N.57, B:V.158, B:W.162, B:W.162, B:V.187, A:T.143, A:L.146 Hydrogen bonds: B:S.1, B:H.23, B:V.70 Water bridges: B:N.269, B:N.269 DAO.10: 10 residues within 4Å: Chain A: G.150 Chain B: H.23, F.24, P.25, M.30, V.70, W.186, Q.465, V.476, G.477 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.24, B:W.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bokhove, M. et al., The Quorum-Quenching N-Acyl Homoserine Lactone Acylase Pvdq is an Ntn-Hydrolase with an Unusual Substrate-Binding Pocket. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2009-12-29

Peptides

ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA: A
ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA

ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA

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