SMTL ID : 8hte.1

Crystal structure of an effector mutant in complex with ubiquitin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: S.196, P.197, A.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.71, A:A.198 SO4.2: 4 residues within 4Å: Chain A: F.90, D.91, D.115, G.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.91, A:D.115 Water bridges: A:A.93, A:Q.121

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.22, S.53, S.54 Ligands: NCA.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.22, A:R.22, A:S.54 Water bridges: A:S.54, A:K.179 GOL.6: 3 residues within 4Å: Chain B: R.42, Q.49, R.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.42, B:R.42, B:Q.49, B:R.72, B:R.72

1 x NCA: NICOTINAMIDE(Non-covalent)

NCA.4: 10 residues within 4Å: Chain A: L.21, R.22, T.23, S.54, A.55, T.56, D.91, T.176, A.177 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.177 Hydrogen bonds: A:T.23, A:T.23, A:T.23

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(Covalent)

AR6.5: 5 residues within 4Å: Chain B: F.4, K.6, E.64, S.65, T.66 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.65 Water bridges: B:K.6, B:K.6 Salt bridges: B:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, J. et al., Molecular basis of threonine ADP-ribosylation of ubiquitin by bacterial ARTs. Nat.Chem.Biol. (2024)

Release Date

2023-11-22

Peptides

NAD(+)--protein-threonine ADP-ribosyltransferase: A
Ubiquitin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD(+)--protein-threonine ADP-ribosyltransferase

Ubiquitin

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