MolNFT v1 · #182972 · protein

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

7NAK · NAD(+) hydrolase SARM1: “Cryo-EM structure of activated human SARM1 in complex with nmn and 1AD (TIR:1AD)”. Electron microscopy, 1 ligand (1QD), 16 pockets (best druggability 0.69). MolNFT v1 #182972 on GenesisL1: 3D structure…

PDB: 7NAK
Type: protein
Length: 1,120 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD(+) hydrolase SARM1
EC: 3.2.2.6, 3.2.2.-
UniProt: Q6SZW1
Ligands: 1QD
Pockets: 16 · best druggability 0.69

Structure

electron microscopy · 1 distinct chain · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, G, B, A, E, F, H	NAD(+) hydrolase SARM1 (EC 3.2.2.6, 3.2.2.-)	protein	140	44% helix, 16% strand	Q6SZW1

Ligands and binding sites

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 · ligand · 8 copies · chains D, C, H, G, B, E, A, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	531	0.69	0.79	49	1QD
2	450	0.68	0.79	47	1QD
3	501	0.67	0.78	46	1QD
4	384	0.64	0.78	38	1QD
5	354	0.63	0.78	27	1QD

Interfaces

13 interfaces between chains.

G–E · 723 Å² buried · 3 hydrogen bonds · protein-protein
C–A · 689 Å² buried · 4 hydrogen bonds · protein-protein
D–B · 672 Å² buried · 7 hydrogen bonds · protein-protein
F–H · 655 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 426 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7NAK · Cryo-EM structure of activated human SARM1 in complex with NMN and 1AD (TIR:1AD) · the same entry in another collection · chain D against D, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6SZW1
Elsewhere: RCSB PDB 7NAK · PDBe 7NAK · UniProt Q6SZW1

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