SMTL ID : 7skk.4 (3 other biounits)

pertussis toxin in complex with ADPR and Nicotinamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: S.58, R.59, R.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.59, A:R.60 SO4.2: 1 residues within 4Å: Ligands: AR6.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.15

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.3: 10 residues within 4Å: Chain A: R.11, Y.12, S.54, T.55, S.56, Y.61, T.62, Y.65, E.131 Ligands: AR6.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.61, A:E.131 Hydrogen bonds: A:Y.12, A:Y.12

1 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.4: 19 residues within 4Å: Chain A: R.11, D.13, S.14, R.15, T.26, A.27, W.28, H.37, L.38, T.39, G.40, S.43, Q.44, S.54, Y.61, Y.65, E.131 Ligands: SO4.2, NCA.3 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:D.13, A:S.14, A:R.15, A:A.27, A:S.43, A:Q.44, A:Q.44, A:S.54, A:Y.61, A:E.131 Water bridges: A:R.11, A:Y.12, A:R.15, A:R.15, A:T.26, A:L.38, A:G.40, A:F.52, A:Y.65, A:E.131 Salt bridges: A:R.11, A:R.11 pi-Stacking: A:W.28, A:W.28, A:W.28 pi-Cation interactions: A:R.15, A:R.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakari, M. et al., Crystal structures of pertussis toxin with NAD + and analogs provide structural insights into the mechanism of its cytosolic ADP-ribosylation activity. J.Biol.Chem. (2022)

Release Date

2022-04-13

Peptides

Pertussis toxin subunit 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Pertussis toxin subunit 1

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