SMTL ID : 3x1k.2 (1 other biounit)

crystal structure of Phosphoapantetheine adenylyltransferase PPAT/CoaD with AMP-PNP from Pseudomonas aerugonosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-trimer

Ligands

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 20 residues within 4Å: Chain A: Y.6, P.7, G.8, T.9, F.10, G.16, H.17, L.20, K.41, R.87, G.88, R.90, D.94, E.98, P.119, Y.123, I.126, S.127, S.128, T.129 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:Y.6, A:T.9, A:T.9, A:F.10, A:K.41, A:R.87, A:G.88, A:R.90, A:R.90, A:E.98, A:E.98, A:I.126, A:S.127, A:S.127, A:S.128, A:T.129, A:T.129 Water bridges: A:S.128, A:S.128 Salt bridges: A:H.17, A:K.41 pi-Cation interactions: A:R.90 ANP.9: 20 residues within 4Å: Chain B: Y.6, P.7, G.8, T.9, F.10, G.16, H.17, L.20, K.41, R.87, G.88, R.90, D.94, E.98, P.119, Y.123, I.126, S.127, S.128, T.129 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:T.9, B:T.9, B:T.9, B:F.10, B:K.41, B:R.87, B:G.88, B:R.90, B:R.90, B:D.94, B:Y.123, B:S.128, B:T.129, B:T.129, B:T.129, B:T.129 Water bridges: B:S.128, B:S.128 Salt bridges: B:H.17, B:K.41 pi-Cation interactions: B:R.90 ANP.16: 19 residues within 4Å: Chain C: Y.6, P.7, G.8, T.9, F.10, G.16, H.17, L.20, R.87, G.88, R.90, D.94, E.98, P.119, Y.123, I.126, S.127, S.128, T.129 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.6, C:T.9, C:F.10, C:R.87, C:G.88, C:R.90, C:R.90, C:D.94, C:E.98, C:Y.123, C:S.128, C:S.128, C:T.129, C:R.132 Salt bridges: C:H.17 pi-Cation interactions: C:R.90

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

DMS.2: 8 residues within 4Å: Chain A: A.36, A.37, S.38, P.39, F.69, S.70, T.71 Ligands: DMS.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.37, A:S.38 DMS.3: 7 residues within 4Å: Chain A: P.7, G.8, T.9, A.36, F.69, R.87 Ligands: DMS.2 No protein-ligand interaction detected (PLIP) DMS.5: 3 residues within 4Å: Chain A: N.83, D.111, E.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.83 DMS.10: 5 residues within 4Å: Chain B: K.15, G.18, D.19, E.22, Y.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.22 Salt bridges: B:E.22 DMS.14: 5 residues within 4Å: Chain A: E.133 Chain C: L.72, L.73, Y.97, L.101 No protein-ligand interaction detected (PLIP) DMS.15: 4 residues within 4Å: Chain C: K.15, G.18, D.19, Y.123 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.22 DMS.17: 6 residues within 4Å: Chain B: L.72, L.73, L.101 Chain C: L.130, E.133, I.134 No protein-ligand interaction detected (PLIP)

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 4 residues within 4Å: Chain A: F.69, S.70, T.71, F.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.70, A:S.70, A:T.71 FMT.6: 1 residues within 4Å: Chain A: R.156 No protein-ligand interaction detected (PLIP) FMT.7: 3 residues within 4Å: Chain A: E.155, R.156, K.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.156 FMT.8: 4 residues within 4Å: Chain A: T.58, K.59, L.61, V.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.61

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

PO4.11: 5 residues within 4Å: Chain A: L.72, L.101 Chain B: L.130, E.133, I.134 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.105

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain B: P.7, G.8, A.36, F.69, L.73, R.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.87, B:R.87 GOL.13: 3 residues within 4Å: Chain B: L.27, F.28, D.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.28

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
B

B
C

C
F

Phosphopantetheine adenylyltransferase

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