SMTL ID : 7nak.1

Cryo-EM structure of activated human SARM1 in complex with NMN and 1AD (TIR:1AD)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x 1QD: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(5-iodanylisoquinolin-2-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

1QD.1: 17 residues within 4Å: Chain A: S.540, Y.541, R.542, R.543, D.567, L.571, F.576, L.580, W.611, V.612, E.615 Chain B: I.630, W.635, L.649, F.651, N.652, G.653 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.571, A:F.576, A:F.576 Hydrogen bonds: A:Y.541, A:R.543, A:E.615, A:E.615, B:F.651, B:F.651, B:G.653 Salt bridges: A:R.542 pi-Stacking: B:W.635, B:W.635 Halogen bonds: B:N.652 1QD.2: 17 residues within 4Å: Chain B: S.540, Y.541, R.542, R.543, D.567, L.571, F.576, L.580, D.610, W.611, V.612, E.615 Chain H: W.635, L.649, F.651, N.652, G.653 14 PLIP interactions: 5 interactions with chain H, 9 interactions with chain B Hydrogen bonds: H:F.651, H:G.653, B:Y.541, B:R.543, B:D.610, B:E.615 pi-Stacking: H:W.635, H:W.635 Halogen bonds: H:N.652 Hydrophobic interactions: B:L.571, B:F.576, B:F.576 Salt bridges: B:R.542 pi-Cation interactions: B:R.543 1QD.3: 20 residues within 4Å: Chain A: I.630, W.635, L.649, T.650, F.651, N.652, G.653 Chain C: S.540, Y.541, R.542, R.543, N.544, D.567, L.571, F.576, L.580, D.610, W.611, V.612, E.615 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:F.576 Hydrogen bonds: C:S.540, C:Y.541, C:R.543, C:R.543, C:D.610, C:E.615, C:E.615, A:F.651, A:F.651, A:G.653 Salt bridges: C:R.542 pi-Stacking: C:W.611, A:W.635, A:W.635, A:W.635 pi-Cation interactions: C:R.543 Halogen bonds: A:N.652 1QD.4: 19 residues within 4Å: Chain D: S.540, Y.541, R.542, R.543, D.567, L.571, F.576, L.580, K.601, D.610, W.611, V.612, E.615 Chain F: I.630, W.635, L.649, F.651, N.652, G.653 13 PLIP interactions: 6 interactions with chain F, 7 interactions with chain D Hydrogen bonds: F:F.651, F:G.653, D:Y.541, D:R.543, D:E.615 pi-Stacking: F:W.635, F:W.635, F:W.635 Halogen bonds: F:N.652 Salt bridges: D:R.542, D:K.601, D:K.601 pi-Cation interactions: D:R.543 1QD.5: 18 residues within 4Å: Chain D: I.630, W.635, L.649, F.651, N.652, G.653 Chain E: S.540, Y.541, R.542, R.543, D.567, L.571, F.576, L.580, K.601, W.611, V.612, E.615 13 PLIP interactions: 5 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:F.651, D:G.653, E:Y.541, E:R.543, E:E.615 pi-Stacking: D:W.635, D:W.635 Halogen bonds: D:N.652 Hydrophobic interactions: E:F.576 Salt bridges: E:R.542, E:K.601, E:K.601 pi-Cation interactions: E:R.543 1QD.6: 11 residues within 4Å: Chain F: S.540, Y.541, R.542, R.543, D.567, L.571, F.576, L.580, W.611, V.612, E.615 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:L.571, F:F.576, F:F.576 Hydrogen bonds: F:Y.541, F:R.543, F:R.543, F:E.615, F:E.615 Salt bridges: F:R.542 pi-Cation interactions: F:R.543 1QD.7: 17 residues within 4Å: Chain E: I.630, W.635, L.649, F.651, N.652, G.653 Chain G: S.540, Y.541, R.542, R.543, D.567, L.571, F.576, L.580, W.611, V.612, E.615 14 PLIP interactions: 9 interactions with chain G, 5 interactions with chain E Hydrophobic interactions: G:F.576, G:L.580 Hydrogen bonds: G:S.540, G:Y.541, G:R.543, G:R.543, G:E.615, E:F.651, E:G.653 Salt bridges: G:R.542 pi-Cation interactions: G:R.543 pi-Stacking: E:W.635, E:W.635, E:W.635 1QD.8: 14 residues within 4Å: Chain H: S.540, Y.541, R.542, R.543, N.544, D.567, L.571, F.576, L.580, K.601, D.610, W.611, V.612, E.615 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:L.571, H:F.576, H:W.611 Hydrogen bonds: H:Y.541, H:R.543, H:D.610 Salt bridges: H:R.542, H:K.601

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, Y. et al., Structural basis of SARM1 activation, substrate recognition, and inhibition by small molecules. Mol.Cell (2022)

Release Date

2022-03-23

Peptides

NAD(+) hydrolase SARM1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
G

D
B

E
A

F
E

G
F

H
H

NAD(+) hydrolase SARM1

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