SMTL ID : 5zq7.1

SidE-Ubi-NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: Q.488, H.494, T.495, N.498, Q.502, R.504, F.540, R.541, G.542, L.543, D.544, L.545, F.549, V.588, S.595, T.596, V.602, P.603, F.607, E.635, E.637 Chain B: R.75 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.602, A:E.637 Hydrogen bonds: A:Q.488, A:N.498, A:R.504, A:G.542, A:G.542, A:D.544, A:D.544, A:V.588, A:S.595 Salt bridges: A:R.541, A:R.541 pi-Cation interactions: A:R.504 NAD.3: 21 residues within 4Å: Chain C: Q.52, R.75 Chain D: Q.488, H.494, N.498, Q.502, R.504, F.540, R.541, G.542, L.543, D.544, F.549, V.588, S.595, T.596, V.602, P.603, F.607, E.635, E.637 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.602 Hydrogen bonds: D:H.494, D:N.498, D:Q.502, D:R.504, D:R.504, D:F.540, D:R.541, D:G.542, D:D.544, D:D.544, D:V.588, D:S.595, D:E.637 Salt bridges: D:R.541, D:R.541 pi-Cation interactions: D:R.504

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 10 residues within 4Å: Chain A: Y.123, W.170, N.180, Q.181, H.183, M.184, L.187, K.191, Y.200, Q.204 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.123, A:Y.123, A:D.165, A:N.180, A:Y.200, A:Y.200, A:Q.204 Salt bridges: A:K.191 pi-Stacking: A:W.170 AMP.4: 8 residues within 4Å: Chain D: Y.123, W.170, N.180, Q.181, H.183, M.184, Y.200, Q.204 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:W.170, D:Y.200, D:Q.204 pi-Stacking: D:W.170, D:W.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE. Cell (2018)

Release Date

2018-05-23

Peptides

SidE: AD
Ubiquitin: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

C
D

SidE

Ubiquitin

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