SMTL ID : 4ruk.2 (1 other biounit)

crystal structure of Phosphoapantetheine adenylyltransferase PPAT/CoaD with CoA and pyrophosphate from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

3 x COA: COENZYME A(Non-covalent)

COA.1: 19 residues within 4Å: Chain A: P.7, G.8, T.9, H.17, A.36, K.41, F.69, T.71, L.72, L.73, R.87, Y.97, L.101, S.127, S.128, T.129, R.132 Chain C: E.133, L.137 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.69, A:L.73 Hydrogen bonds: A:T.9, A:T.9, A:T.9, A:F.10, A:L.73, A:Y.97, A:S.128, A:T.129, A:T.129, A:T.129, A:R.132 Water bridges: A:A.74, A:R.132 Salt bridges: A:H.17, A:K.41, A:K.41, A:R.87, A:R.87, A:R.90 pi-Cation interactions: A:K.41 COA.8: 22 residues within 4Å: Chain A: E.133, I.134, L.137 Chain B: P.7, G.8, T.9, A.36, K.41, F.69, L.72, L.73, R.87, R.90, S.93, D.94, Y.97, L.101, S.127, S.128, T.129 Ligands: POP.9, DMS.10 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.9, B:T.9, B:T.9, B:L.73, B:S.93, B:Y.97, B:S.128, B:T.129, B:T.129 Water bridges: B:F.10, B:A.74 Salt bridges: B:K.41, B:K.41, B:R.87, B:R.87, B:R.90 Hydrophobic interactions: A:L.137 COA.15: 23 residues within 4Å: Chain B: L.137 Chain C: P.7, G.8, T.9, F.10, H.17, A.36, A.37, S.38, K.41, F.69, S.70, T.71, L.72, L.73, R.87, Y.97, L.101, S.127, S.128, T.129 Ligands: CA.16, ACT.19 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.101 Hydrogen bonds: C:T.9, C:T.9, C:F.10, C:S.38, C:K.41, C:K.41, C:T.71, C:L.73, C:R.87, C:S.128, C:T.129, C:T.129 Water bridges: C:D.11 Salt bridges: C:H.17, C:K.41, C:K.41, C:R.87 pi-Cation interactions: C:K.41

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

FMT.2: 4 residues within 4Å: Chain A: S.25, R.26, L.61, N.63 No protein-ligand interaction detected (PLIP) FMT.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.4: 3 residues within 4Å: Chain A: V.66, V.67, G.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.68, A:G.68 FMT.5: 3 residues within 4Å: Chain A: Q.55, E.65, V.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.55, A:V.66 FMT.6: 3 residues within 4Å: Chain A: E.65, V.67, Q.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.80 FMT.7: 5 residues within 4Å: Chain A: D.140, I.141, S.142, K.143, F.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.140, A:S.142, A:K.143, A:K.143 FMT.12: 2 residues within 4Å: Chain B: S.70 Ligands: DMS.11 No protein-ligand interaction detected (PLIP) FMT.14: 3 residues within 4Å: Chain A: K.40 Chain C: R.132, E.133 No protein-ligand interaction detected (PLIP) FMT.18: 4 residues within 4Å: Chain C: S.25, R.26, L.27, F.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.28

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.9: 8 residues within 4Å: Chain B: Y.6, G.16, H.17, L.20, R.87, G.88, R.90 Ligands: COA.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.6, B:G.88, B:R.90 Water bridges: B:H.17, B:S.128 Salt bridges: B:H.17, B:R.87, B:R.90

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

DMS.10: 8 residues within 4Å: Chain A: L.137 Chain B: A.36, A.37, S.38, F.69, S.70, T.71 Ligands: COA.8 No protein-ligand interaction detected (PLIP) DMS.11: 6 residues within 4Å: Chain B: G.68, F.69, S.70, T.71, F.76 Ligands: FMT.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.70, B:T.71 Salt bridges: B:E.79 DMS.17: 5 residues within 4Å: Chain C: K.15, G.18, D.19, E.22, Y.123 1 PLIP interactions: 1 interactions with chain C pi-Cation interactions: C:Y.123

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 2 residues within 4Å: Chain B: K.40, K.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.41

1 x CA: CALCIUM ION(Non-covalent)

CA.16: 4 residues within 4Å: Chain C: H.17, R.90, S.128 Ligands: COA.15 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.19: 7 residues within 4Å: Chain C: Y.6, P.7, H.17, R.87, G.88, R.90 Ligands: COA.15 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.6 Hydrogen bonds: C:Y.6, C:Y.6, C:G.88 Salt bridges: C:R.87, C:R.90

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
D

C
E

Phosphopantetheine adenylyltransferase

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