Research workbench
Crystal structure of the ligand-free arm domain from drosophila SARM1
Analyse Crystal structure of the ligand-free arm domain from drosophila SARM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LCY
- Type
- protein
- Length
- 958 residues
- Chains
- 3
- 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
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform B of NAD(+) hydrolase SARM1 (EC 3.2.2.6) | protein | 331 | 73% helix, 1% strand | Q6IDD9 |
| B | Isoform B of NAD(+) hydrolase SARM1 (EC 3.2.2.6) | protein | 310 | 70% helix, 0% strand | Q6IDD9 |
| C | Isoform B of NAD(+) hydrolase SARM1 (EC 3.2.2.6) | protein | 317 | 70% helix, 0% strand | Q6IDD9 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.74 | 0.79 | 49 | empty |
| 2 | 693 | 0.70 | 0.77 | 51 | empty |
| 3 | 717 | 0.68 | 0.76 | 54 | empty |
| 4 | 55 | 0.57 | 0.90 | 18 | empty |
| 5 | 143 | 0.52 | 0.80 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1005 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1000 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7LCY · Crystal structure of the ligand-free ARM domain from Drosophila SARM1 · 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 A against A, TM-score 0.97
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 7LCY · PDBe 7LCY · UniProt Q6IDD9
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