MolNFT v1 · #181804 · protein
Crystal structure of the arm domain from drosophila SARM1 in complex with vmn
7M6K · Isoform B of NAD(+) hydrolase SARM1: “Crystal structure of the arm domain from drosophila SARM1 in complex with vmn”. X-ray diffraction, 2 ligands (YRJ, NA), 5 pockets (best druggability 0.84). MolNFT v1 #181804 on GenesisL1: 3D…
- PDB
- 7M6K
- Type
- protein
- Length
- 609 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
- YRJ, NA
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 79% 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 | 79% helix, 0% strand | Q6IDD9 |
| B | Isoform B of NAD(+) hydrolase SARM1 (EC 3.2.2.6) | protein | 306 | 78% helix, 0% strand | Q6IDD9 |
Ligands and binding sites
- YRJ · 3-({[(4-nitrophenyl)carbamoyl]amino}methyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.84 | 0.88 | 67 | YRJ |
| 2 | 415 | 0.79 | 0.88 | 44 | YRJ |
| 3 | 84 | 0.42 | 0.79 | 21 | empty |
| 4 | 72 | 0.37 | 0.77 | 22 | NA |
| 5 | 51 | 0.31 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 539 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7M6K · Crystal structure of the ARM domain from Drosophila SARM1 in complex with VMN · 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 0.94
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 7M6K · PDBe 7M6K · UniProt Q6IDD9
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