SMTL ID : 2y4o.1

Crystal Structure of PaaK2 in complex with phenylacetyl adenylate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: A.210, S.212, L.214, V.236, G.237 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.212, A:L.214, A:V.236, H2O.10, H2O.11 MG.11: 5 residues within 4Å: Chain B: A.210, S.212, L.214, V.236, G.237 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.212, B:L.214, B:V.236, H2O.27, H2O.27

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: A.221, G.342, N.344 Ligands: DLL.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.221, A:G.342, DLL.3 K.12: 4 residues within 4Å: Chain B: A.221, G.342, N.344 Ligands: DLL.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.221, B:G.342, DLL.4

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

DLL.3: 21 residues within 4Å: Chain A: F.143, F.148, T.149, G.150, G.220, A.221, E.222, P.223, D.242, I.243, Y.244, G.245, L.246, S.247, P.252, D.312, I.330, R.333, I.339, N.344 Ligands: K.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.143, A:F.143, A:F.148, A:A.221, A:I.243, A:P.252 Hydrogen bonds: A:A.221, A:I.243, A:Y.244, A:G.245, A:S.247, A:S.247, A:D.312, A:R.333, A:N.344 Water bridges: A:S.100, A:D.312 pi-Stacking: A:Y.244 DLL.4: 21 residues within 4Å: Chain B: F.143, F.148, T.149, G.150, G.220, A.221, E.222, P.223, D.242, I.243, Y.244, G.245, L.246, S.247, P.252, D.312, I.330, R.333, I.339, N.344 Ligands: K.12 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.148, B:A.221, B:P.252 Hydrogen bonds: B:A.221, B:D.242, B:G.245, B:S.247, B:S.247, B:D.312, B:R.333, B:N.344 Water bridges: B:K.75, B:D.312 pi-Stacking: B:F.143, B:Y.244

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

PEG.5: 5 residues within 4Å: Chain A: Y.156, R.160 Chain B: Y.156, E.159, R.160 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.160, B:R.160 Water bridges: A:E.159, A:E.159, A:R.160, B:E.159, B:R.160 PEG.6: 3 residues within 4Å: Chain B: Y.41, R.48, D.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.48 Water bridges: B:Y.41 PEG.7: 7 residues within 4Å: Chain B: A.68, K.69, F.70, P.71, F.72, T.281, R.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.281, B:R.307 Water bridges: B:F.72 PEG.8: 3 residues within 4Å: Chain B: H.46, R.49, N.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.49, B:N.81, B:N.81 PEG.9: 6 residues within 4Å: Chain B: W.224, T.225, Q.226, R.229, D.242, K.329 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.226, B:K.329 Water bridges: B:W.224, B:R.229, B:R.229, B:D.242, B:A.328, B:I.330

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

BME.10: 6 residues within 4Å: Chain B: L.25, Q.26, Q.29, E.269, A.323, R.325 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.26, B:Q.29, B:Q.29 Water bridges: B:R.325

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

2011-03-09

Peptides

PHENYLACETATE-COENZYME A LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHENYLACETATE-COENZYME A LIGASE