SMTL ID : 2y27.1

crystal structure of PaaK1 in complex with ATP from Burkholderia cenocepacia

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

9 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 6 residues within 4Å: Chain A: L.194, A.229, I.230, R.233, P.360 Ligands: BME.6 No protein-ligand interaction detected (PLIP) SCN.2: 2 residues within 4Å: Chain A: W.33, T.297 No protein-ligand interaction detected (PLIP) SCN.3: 1 residues within 4Å: Chain A: L.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.12 SCN.4: 5 residues within 4Å: Chain A: P.165, F.166, Q.170 Chain B: G.144, L.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.145 Water bridges: B:F.146 SCN.12: 2 residues within 4Å: Chain A: R.307 Ligands: PG4.7 No protein-ligand interaction detected (PLIP) SCN.13: 5 residues within 4Å: Chain A: K.173 Chain B: A.97, P.105, V.107, L.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.173 SCN.14: 5 residues within 4Å: Chain A: A.97, P.105, V.107 Chain B: K.173, L.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.173 SCN.15: 6 residues within 4Å: Chain B: L.194, A.229, I.230, R.233, P.360 Ligands: BME.24 No protein-ligand interaction detected (PLIP) SCN.16: 2 residues within 4Å: Chain B: D.58, R.67 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.67

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 12 residues within 4Å: Chain A: F.146, T.147, A.219, I.241, Y.242, G.243, L.244, S.245, G.249, P.250, K.427 Ligands: ATP.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.219, A:I.241, A:K.427 GOL.17: 8 residues within 4Å: Chain B: S.191, L.194, H.361, I.421, E.422, R.423, S.424, A.428 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.191, B:H.361 Water bridges: B:S.195, B:R.430 GOL.18: 9 residues within 4Å: Chain B: F.146, G.218, A.219, I.241, Y.242, G.243, P.250, K.427 Ligands: ATP.25 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.219, B:I.241, B:K.427, B:K.427 GOL.19: 2 residues within 4Å: Chain B: R.47, E.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.47, B:E.51 GOL.20: 4 residues within 4Å: Chain B: H.41, P.43, F.85, V.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.85 Water bridges: B:V.87

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

BME.6: 5 residues within 4Å: Chain A: R.233, A.359, C.382, P.383 Ligands: SCN.1 No protein-ligand interaction detected (PLIP) BME.21: 4 residues within 4Å: Chain B: I.15, R.30, D.268, H.269 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.30 BME.22: 4 residues within 4Å: Chain B: T.17, T.318, R.320, T.321 No protein-ligand interaction detected (PLIP) BME.23: 4 residues within 4Å: Chain B: G.100, G.103, K.104, P.105 No protein-ligand interaction detected (PLIP) BME.24: 5 residues within 4Å: Chain B: R.233, A.359, C.382, P.383 Ligands: SCN.15 2 PLIP interactions: 2 interactions with chain B Water bridges: B:L.358, B:L.358

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 10 residues within 4Å: Chain A: A.52, S.66, R.67, F.68, P.69, F.70, T.279, E.281, R.305 Ligands: SCN.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.70

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.8: 24 residues within 4Å: Chain A: K.73, S.98, S.99, G.100, T.101, T.102, F.146, G.218, A.219, E.220, P.221, D.240, I.241, Y.242, G.243, L.244, S.245, E.246, D.310, I.328, R.331, K.427 Ligands: GOL.5, MG.9 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:S.98, A:S.99, A:G.100, A:T.101, A:T.101, A:T.101, A:T.102, A:T.102, A:A.219, A:I.241, A:Y.242, A:G.243, A:S.245, A:S.245, A:D.310, A:R.331 Water bridges: A:K.73, A:R.77, A:T.106, A:R.331, A:R.331, A:R.331, A:R.331, A:R.331, A:R.331 Salt bridges: A:K.73, A:R.331, A:K.427, A:K.427 ATP.25: 24 residues within 4Å: Chain B: K.73, S.98, S.99, G.100, T.101, T.102, F.146, G.218, A.219, E.220, P.221, D.240, I.241, Y.242, G.243, L.244, S.245, E.246, D.310, I.328, R.331, K.427 Ligands: GOL.18, MG.27 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:S.98, B:S.99, B:G.100, B:T.101, B:T.101, B:T.102, B:T.102, B:A.219, B:D.240, B:G.243, B:S.245, B:S.245, B:D.310, B:R.331 Water bridges: B:R.77, B:T.106, B:E.246, B:R.331, B:R.331, B:R.331, B:R.331, B:R.331, B:R.331, B:K.427 Salt bridges: B:K.73, B:R.331, B:K.427, B:K.427

6 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: K.73 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.10: 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.1, H2O.2, H2O.5, H2O.10 MG.11: 5 residues within 4Å: Chain A: V.208, S.210, L.212, M.234, G.235 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.208, A:S.210, A:L.212, A:G.235, H2O.14 MG.26: 3 residues within 4Å: Chain B: Q.355, R.356, L.358 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:Q.355, B:L.358, H2O.20, H2O.28, H2O.29 MG.27: 2 residues within 4Å: Chain B: R.331 Ligands: ATP.25 No protein-ligand interaction detected (PLIP) MG.28: 6 residues within 4Å: Chain B: P.207, V.208, S.210, L.212, M.234, G.235 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.208, B:S.210, B:L.212, B:M.234

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

2011-05-04

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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