SMTL ID : 3l91.1

Structure of Pseudomonas aerugionsa PvdQ bound to octanoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: A.47, I.50, V.51, W.130, R.132, I.134 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: R.54, E.56, R.141 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: L.74, I.78, V.160 Chain B: H.121 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: R.13, R.23 Chain B: R.541 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: E.149 Chain B: V.70, W.186 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: Y.17 Chain B: Q.34, G.496, L.497, Q.514, Q.524, T.525, L.526, P.527 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: S.68, A.69, R.145 Chain B: P.25, N.27, G.28, A.29, M.30 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: R.42, L.43, D.44, S.61, N.166, Q.167 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain B: G.41 Ligands: EDO.11 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: T.38, P.40, G.41, R.42, L.43, D.44 Ligands: EDO.10 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: R.62, E.194, F.487, P.488, E.489, G.491, P.492 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: P.488, E.490, G.491, P.492, K.493, Q.532 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: T.156, R.157, A.246, Q.247 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: R.149, A.238, W.239, R.241, A.248, G.249 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: F.380, A.381, L.383, G.385, A.386, W.387 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: L.53, V.55, N.57, V.158, W.162 Ligands: OCA.6 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: D.513, E.516 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: V.371, R.375, S.428, I.430, R.468 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: L.364, D.365, G.437, D.438, A.450 Ligand excluded by PLIP

1 x OCA: OCTANOIC ACID (CAPRYLIC ACID)(Non-covalent)

OCA.6: 13 residues within 4Å: Chain A: L.146 Chain B: S.1, P.22, F.24, N.57, I.58, H.68, T.69, V.70, W.162, W.186, V.187 Ligands: EDO.17 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.24, B:F.24, B:I.58, B:H.68, B:W.162, B:W.186, A:L.146 Hydrogen bonds: B:S.1, B:V.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drake, E.J. et al., Structural characterization and high-throughput screening of inhibitors of PvdQ, an NTN hydrolase involved in pyoverdine synthesis. Acs Chem.Biol. (2011)

Release Date

2011-01-19

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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