SMTL ID : 9l2d.1

Structure of SARM1 bound to M1 in the intermediate state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.83 Å

Oligo State

homo-octamer

Ligands

8 x 01: [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(3-sulfanylpyridin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

01.1: 10 residues within 4Å: Chain A: W.103, R.110, E.149, Q.150, L.152, V.153, A.154, R.157, H.190, K.193 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.190, A:H.190 Salt bridges: A:R.110, A:R.157, A:K.193 pi-Stacking: A:W.103 01.2: 10 residues within 4Å: Chain B: W.103, R.110, E.149, Q.150, L.152, V.153, A.154, R.157, H.190, K.193 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:L.152, B:L.152, B:A.154, B:H.190, B:H.190 Salt bridges: B:R.110, B:R.157, B:K.193 pi-Stacking: B:W.103, B:W.103 01.3: 10 residues within 4Å: Chain C: W.103, R.110, E.149, Q.150, L.152, V.153, A.154, R.157, H.190, K.193 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.110, C:L.152, C:L.152, C:H.190, C:H.190 Salt bridges: C:R.110, C:R.157, C:K.193 pi-Stacking: C:W.103, C:W.103 01.4: 9 residues within 4Å: Chain D: W.103, R.110, E.149, Q.150, L.152, V.153, R.157, H.190, K.193 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.110, D:L.152, D:H.190, D:H.190 Salt bridges: D:R.110, D:R.157, D:K.193 pi-Stacking: D:W.103, D:W.103 01.5: 9 residues within 4Å: Chain E: W.103, R.110, E.149, Q.150, L.152, V.153, R.157, H.190, K.193 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:R.110, E:L.152, E:H.190, E:H.190 Salt bridges: E:R.110, E:R.157, E:K.193 pi-Stacking: E:W.103, E:W.103 01.6: 9 residues within 4Å: Chain F: W.103, R.110, E.149, Q.150, L.152, V.153, R.157, H.190, K.193 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:L.152, F:H.190, F:H.190 Salt bridges: F:R.110, F:R.157, F:K.193 pi-Stacking: F:W.103, F:W.103 01.7: 9 residues within 4Å: Chain G: W.103, R.110, E.149, Q.150, L.152, V.153, R.157, H.190, K.193 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:R.110, G:L.152, G:H.190, G:H.190 Salt bridges: G:R.157, G:K.193 pi-Stacking: G:W.103, G:W.103 01.8: 9 residues within 4Å: Chain H: W.103, R.110, E.149, Q.150, L.152, V.153, R.157, H.190, K.193 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:L.152, H:H.190, H:H.190 Salt bridges: H:R.110, H:R.157, H:K.193 pi-Stacking: H:W.103, H:W.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y. et al., Stepwise Activation of SARM1 by a Biosynthetic NMN mimic. To Be Published

Release Date

2025-03-12

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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