SMTL ID : 7dn9.4 (3 other biounits)

Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 16 residues within 4Å: Chain A: I.78, N.79, L.90, N.93, E.95, Y.96, L.97, R.116, Y.162, A.163, A.175, Y.178, D.199, Y.201, Y.261, D.263 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.175, A:Y.178, A:Y.261 Hydrogen bonds: A:N.79, A:N.79, A:N.93, A:E.95, A:Y.96, A:Y.96, A:L.97, A:R.116 Salt bridges: A:R.116 pi-Stacking: A:Y.96

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain B: K.14, T.15, T.32 Ligands: GDP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.32

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 17 residues within 4Å: Chain B: L.9, D.10, A.11, A.12, G.13, K.14, T.15, T.16, T.29, N.110, K.111, D.113, L.114, C.143, A.144, T.145 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:A.11, B:A.12, B:G.13, B:K.14, B:T.15, B:T.16, B:T.16, B:T.29, B:N.110, B:K.111, B:K.111, B:A.144, B:T.145, B:T.145 Salt bridges: B:K.14, B:D.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., ARF GTPases activate Salmonella effector SopF to ADP-ribosylate host V-ATPase and inhibit endomembrane damage-induced autophagy. Nat.Struct.Mol.Biol. (2022)

Release Date

2021-12-15

Peptides

Putative cytoplasmic protein: A
ADP-ribosylation factor 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Putative cytoplasmic protein

ADP-ribosylation factor 1

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