Research workbench
Crystal structure of the arm domain from drosophila SARM1 in complex with nmn
Analyse Crystal structure of the arm domain from drosophila SARM1 in complex with nmn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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