SMTL ID : 3x1j.1

Crystal Structure of Phosphopantetheine adenylyltransferase (PPAT/CoaD) with AcCoA from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-trimer

Ligands

3 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 25 residues within 4Å: Chain A: Y.6, P.7, G.8, T.9, F.10, H.17, A.36, K.41, F.69, L.72, L.73, R.87, G.88, R.90, Y.97, L.101, N.105, S.127, S.128, T.129 Chain C: L.130, E.133, I.134, L.137 Ligands: DMS.7 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:P.7, A:T.9, A:T.9, A:H.17, A:L.73, A:G.88, A:R.90, A:N.105, A:S.128, A:T.129, A:T.129, C:E.133 Salt bridges: A:K.41, A:K.41, A:R.87 pi-Stacking: A:H.17 Hydrophobic interactions: C:L.130, C:I.134 ACO.10: 24 residues within 4Å: Chain A: E.133, I.134, L.137 Chain B: Y.6, P.7, G.8, T.9, H.17, A.36, K.41, F.69, T.71, L.72, L.73, A.74, R.87, G.88, R.90, Y.97, L.101, N.105, S.127, S.128, T.129 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.73, B:L.101, B:L.101, A:L.137 Hydrogen bonds: B:Y.6, B:P.7, B:T.9, B:H.17, B:H.17, B:L.73, B:A.74, B:R.87, B:G.88, B:S.128, B:T.129 Salt bridges: B:K.41, B:K.41, B:R.87, B:R.90 pi-Stacking: B:H.17 ACO.14: 27 residues within 4Å: Chain B: L.130, E.133, I.134, L.137 Chain C: Y.6, P.7, G.8, T.9, F.10, H.17, A.36, K.41, F.69, T.71, L.72, L.73, R.87, G.88, R.90, Y.97, L.101, M.104, N.105, I.126, S.127, S.128, T.129 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.101, C:L.101, C:M.104, B:I.134 Hydrogen bonds: C:T.9, C:H.17, C:L.73, C:R.87, C:G.88, C:R.90, C:R.90, C:Y.97, C:S.127, C:S.127, C:S.128, C:T.129, B:E.133 Salt bridges: C:K.41, C:K.41, C:R.87, C:R.87 pi-Stacking: C:H.17

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: G.68, F.69, S.70, T.71, F.76 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.70, A:T.71 Water bridges: A:T.71 PO4.3: 3 residues within 4Å: Chain A: N.83, D.111, E.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.83, A:D.111, A:E.113

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: L.47, G.68, F.69, S.70 Ligands: PO4.2, GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.70, A:S.70, A:S.70 Water bridges: A:G.68, A:G.68 GOL.5: 2 residues within 4Å: Chain A: S.70 Ligands: GOL.4 No protein-ligand interaction detected (PLIP)

8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 2 residues within 4Å: Chain A: E.48, Q.49 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.48 DMS.7: 9 residues within 4Å: Chain A: A.36, A.37, S.38, P.39, F.69, S.70, T.71 Ligands: ACO.1, DMS.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.38 pi-Cation interactions: A:F.69 DMS.8: 5 residues within 4Å: Chain A: K.15, G.18, D.19, E.22, Y.123 No protein-ligand interaction detected (PLIP) DMS.11: 5 residues within 4Å: Chain B: K.15, G.18, D.19, E.22, Y.123 No protein-ligand interaction detected (PLIP) DMS.12: 2 residues within 4Å: Chain B: R.26, L.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.26 DMS.13: 6 residues within 4Å: Chain B: G.68, F.69, S.70, T.71, F.76, E.79 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.71 Salt bridges: B:E.79 DMS.15: 5 residues within 4Å: Chain C: K.15, G.18, D.19, E.22, Y.123 No protein-ligand interaction detected (PLIP) DMS.16: 4 residues within 4Å: Chain A: P.39 Chain C: E.133, L.137 Ligands: DMS.7 No protein-ligand interaction detected (PLIP)

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

PEG.9: 3 residues within 4Å: Chain A: E.155, R.156, K.158 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chatterjee, R. et al., Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa. Biochim.Biophys.Acta (2016)

Release Date

2015-11-25

Peptides

Phosphopantetheine adenylyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Phosphopantetheine adenylyltransferase

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