SMTL ID : 7nal.1

Cryo-EM structure of activated human SARM1 in complex with NMN and 1AD (ARM and SAM domains)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-covalent)

NMN.1: 16 residues within 4Å: Chain A: W.76, R.83, E.122, Q.123, I.124, L.125, V.126, R.130, H.163, K.166, S.289, D.290, T.291, Q.293, G.294, D.299 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.76 Hydrogen bonds: A:R.83, A:E.122, A:L.125, A:R.130, A:Q.293, A:G.294, A:G.294 Salt bridges: A:R.83, A:K.166 pi-Stacking: A:W.76 NMN.2: 17 residues within 4Å: Chain B: W.76, R.83, E.122, Q.123, I.124, L.125, V.126, R.130, H.163, K.166, S.289, D.290, T.291, S.292, Q.293, G.294, D.299 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.76 Hydrogen bonds: B:R.83, B:E.122, B:L.125, B:R.130, B:Q.293, B:G.294, B:G.294, B:D.299 Salt bridges: B:R.83, B:K.166 pi-Stacking: B:W.76 NMN.3: 17 residues within 4Å: Chain C: W.76, R.83, E.122, Q.123, I.124, L.125, V.126, R.130, H.163, K.166, S.289, D.290, T.291, S.292, Q.293, G.294, D.299 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.76 Hydrogen bonds: C:R.83, C:E.122, C:L.125, C:R.130, C:Q.293, C:G.294, C:G.294 Salt bridges: C:R.83, C:K.166 pi-Stacking: C:W.76 NMN.4: 17 residues within 4Å: Chain D: W.76, R.83, E.122, Q.123, I.124, L.125, V.126, R.130, H.163, K.166, S.289, D.290, T.291, S.292, Q.293, G.294, D.299 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.76 Hydrogen bonds: D:R.83, D:E.122, D:L.125, D:R.130, D:Q.293, D:G.294, D:G.294, D:D.299 Salt bridges: D:R.83, D:K.166 pi-Stacking: D:W.76 NMN.5: 16 residues within 4Å: Chain E: W.76, R.83, E.122, Q.123, I.124, L.125, V.126, R.130, H.163, K.166, S.289, D.290, T.291, Q.293, G.294, D.299 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:W.76 Hydrogen bonds: E:R.83, E:E.122, E:L.125, E:R.130, E:Q.293, E:G.294, E:G.294 Salt bridges: E:R.83, E:K.166 pi-Stacking: E:W.76 NMN.6: 17 residues within 4Å: Chain F: W.76, R.83, E.122, Q.123, I.124, L.125, V.126, R.130, H.163, K.166, S.289, D.290, T.291, S.292, Q.293, G.294, D.299 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:W.76 Hydrogen bonds: F:R.83, F:E.122, F:L.125, F:R.130, F:Q.293, F:G.294, F:G.294, F:D.299 Salt bridges: F:R.83, F:K.166 pi-Stacking: F:W.76 NMN.7: 16 residues within 4Å: Chain G: W.76, R.83, E.122, Q.123, I.124, L.125, V.126, R.130, H.163, K.166, S.289, D.290, T.291, Q.293, G.294, D.299 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:W.76 Hydrogen bonds: G:R.83, G:E.122, G:L.125, G:R.130, G:Q.293, G:G.294, G:G.294 Salt bridges: G:R.83, G:K.166 pi-Stacking: G:W.76 NMN.8: 17 residues within 4Å: Chain H: W.76, R.83, E.122, Q.123, I.124, L.125, V.126, R.130, H.163, K.166, S.289, D.290, T.291, S.292, Q.293, G.294, D.299 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:W.76 Hydrogen bonds: H:R.83, H:E.122, H:L.125, H:R.130, H:Q.293, H:G.294, H:G.294, H:D.299 Salt bridges: H:R.83, H:K.166 pi-Stacking: H:W.76

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
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

NAD(+) hydrolase SARM1

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