MolNFT v1 · #186877 · protein
Crystal structure of the arm domain from drosophila SARM1 in complex with namn
7RTC · NAD(+) hydrolase SARM1: “Crystal structure of the arm domain from drosophila SARM1 in complex with namn”. X-ray diffraction, 1 ligand (NCN), 15 pockets (best druggability 0.73). MolNFT v1 #186877 on GenesisL1: 3D structure, binding…
- PDB
- 7RTC
- Type
- protein
- Length
- 993 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(+) hydrolase SARM1
- EC
- 3.2.2.6
- UniProt
- Q6IDD9
- Ligands
- NCN
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | NAD(+) hydrolase SARM1 (EC 3.2.2.6) | protein | 331 | 72% helix, 0% strand | Q6IDD9 |
Ligands and binding sites
- NCN · Nicotinate mononucleotide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.73 | 0.79 | 48 | NCN |
| 2 | 750 | 0.72 | 0.78 | 50 | NCN |
| 3 | 769 | 0.72 | 0.78 | 49 | NCN |
| 4 | 121 | 0.54 | 0.82 | 20 | empty |
| 5 | 93 | 0.52 | 0.83 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 975 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7RTC · Crystal structure of the ARM domain from Drosophila SARM1 in complex with NaMN · 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 0.96
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 7RTC · PDBe 7RTC · UniProt Q6IDD9
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