MolNFT v1 · #171763 · protein

HSARM1 grafix-ed

6ZFX · NAD(+) hydrolase SARM1: “HSARM1 grafix-ed”. Electron microscopy, 1 ligand (S1N), 20 pockets (best druggability 0.83). MolNFT v1 #171763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZFX
Type: protein
Length: 5,080 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: S1N
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 63% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	NAD(+) hydrolase SARM1 (EC 3.2.2.6, 3.2.2.-)	protein	635	63% helix, 3% strand	Q6SZW1

Ligands and binding sites

S1N · (~{E})-4-methylnon-4-enedial · ligand · 16 copies · chains A, H, B, C, D, E, F, G

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	994	0.83	0.84	117	S1N
2	1171	0.83	0.84	139	S1N
3	892	0.82	0.85	97	S1N
4	837	0.82	0.84	94	S1N
5	812	0.81	0.85	96	S1N

Interfaces

16 interfaces between chains.

B–C · 2403 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 2397 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2396 Å² buried · 25 hydrogen bonds · protein-protein
A–H · 2396 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2395 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 covalent (covalent ligand).

Compared structures

6ZFX · hSARM1 GraFix-ed · the same entry in another collection · chain H against H, TM-score 1.00
Q6SZW1 · AlphaFold monomer V2.0 prediction for NAD(+) hydrolase SARM1 (Q6SZW1) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 6ZFX · PDBe 6ZFX · UniProt Q6SZW1

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