MolNFT v1 · #180851 · protein
Crystal structure of the arm domain from drosophila SARM1 in complex with nmn
7LCZ · Isoform B of NAD(+) hydrolase SARM1: “Crystal structure of the arm domain from drosophila SARM1 in complex with nmn”. X-ray diffraction, 2 ligands (NMN, NA), 6 pockets (best druggability 0.84). MolNFT v1 #180851 on GenesisL1: 3D…
- PDB
- 7LCZ
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform B of NAD(+) hydrolase SARM1
- EC
- 3.2.2.6
- UniProt
- Q6IDD9
- Ligands
- NMN, NA
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform B of NAD(+) hydrolase SARM1 (EC 3.2.2.6) | protein | 303 | 78% helix, 0% strand | Q6IDD9 |
| B | Isoform B of NAD(+) hydrolase SARM1 (EC 3.2.2.6) | protein | 307 | 78% helix, 0% strand | Q6IDD9 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.84 | 0.87 | 67 | NMN |
| 2 | 453 | 0.80 | 0.88 | 47 | NMN, NA |
| 3 | 80 | 0.39 | 0.78 | 21 | empty |
| 4 | 71 | 0.39 | 0.79 | 20 | empty |
| 5 | 56 | 0.32 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 655 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7LCZ · Crystal structure of the ARM domain from Drosophila SARM1 in complex with NMN · the same entry in another collection · chain A against A, TM-score 1.00
- Q6IDD9 · AlphaFold monomer V2.0 prediction for NAD(+) hydrolase SARM1 (Q6IDD9) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q6IDD9
- Elsewhere: RCSB PDB 7LCZ · PDBe 7LCZ · UniProt Q6IDD9
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