SMTL ID : 2y4n.1

PaaK1 in complex with phenylacetyl adenylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: Q.355, R.356, L.358 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:Q.355, A:L.358, H2O.6, H2O.7, H2O.9, H2O.13 MG.2: 4 residues within 4Å: Chain A: V.208, Q.209, S.210, L.212 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.208, A:S.210, H2O.1, H2O.14 MG.6: 3 residues within 4Å: Chain B: Q.355, R.356, L.358 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:Q.355, B:L.358, H2O.18, H2O.20, H2O.22, H2O.23 MG.7: 4 residues within 4Å: Chain B: V.208, Q.209, S.210, L.212 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:V.208, B:S.210, H2O.17, H2O.20, H2O.25

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 10 residues within 4Å: Chain A: N.224, R.227, E.255, K.260, D.261, G.262, L.315, R.324, E.326, K.327 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.224, A:R.227, A:G.262, A:R.324, A:K.327

3 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 7 residues within 4Å: Chain A: D.198, R.233, L.358, A.359, P.360, C.382, P.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.201 Water bridges: A:R.233 BME.10: 6 residues within 4Å: Chain B: A.97, S.99, G.144, L.145, F.146 Ligands: PAC.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.99 Water bridges: A:K.173 BME.11: 4 residues within 4Å: Chain B: E.201, R.233, A.359, C.382 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.201

2 x DLL: 5'-O-[HYDROXY(PHENYLACETYL)PHOSPHORYL]ADENOSINE(Non-covalent)

DLL.5: 20 residues within 4Å: Chain A: Y.141, F.146, T.147, G.148, G.218, A.219, E.220, P.221, D.240, I.241, Y.242, G.243, L.244, S.245, E.246, P.250, D.310, I.328, R.331, K.427 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.141, A:F.146, A:A.219, A:P.250 Hydrogen bonds: A:A.219, A:E.220, A:I.241, A:G.243, A:S.245, A:S.245, A:D.310, A:R.331 Water bridges: A:K.327, A:I.328, A:K.427, A:K.427 Salt bridges: A:K.427, A:K.427 DLL.12: 22 residues within 4Å: Chain B: S.98, Y.141, F.146, T.147, G.148, G.218, A.219, E.220, P.221, D.240, I.241, Y.242, G.243, L.244, S.245, E.246, G.249, P.250, D.310, I.328, R.331, K.427 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.146, B:A.219, B:I.241, B:P.250 Hydrogen bonds: B:S.98, B:A.219, B:E.220, B:I.241, B:Y.242, B:Y.242, B:G.243, B:S.245, B:S.245, B:R.331 Water bridges: B:K.327, B:K.427, B:K.427 Salt bridges: B:K.427, B:K.427 pi-Stacking: B:Y.141, B:Y.242

1 x PAC: 2-PHENYLACETIC ACID(Non-covalent)

PAC.8: 6 residues within 4Å: Chain B: S.99, G.142, F.146, G.426, K.427 Ligands: BME.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.427 Hydrogen bonds: B:S.99 Water bridges: B:S.99 Salt bridges: B:K.427 pi-Stacking: B:F.146

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

PGE.9: 7 residues within 4Å: Chain B: A.52, S.66, R.67, F.68, P.69, F.70, R.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.52, B:R.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Law, A. et al., Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-Coa Ligases from the Cystic Fibrosis Pathogen Burkholderia Cenocepacia J2315. J.Biol.Chem. (2011)

Release Date

2011-03-01

Peptides

PHENYLACETATE-COENZYME A LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHENYLACETATE-COENZYME A LIGASE

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