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