MolNFT v1 · #9797 · protein
Crystal structure analysis of the complex of the C domain of synapsin II from rat with ATP
1I7L: “Crystal structure analysis of the complex of the C domain of synapsin II from rat with ATP”. X-ray diffraction, 1 ligand (ATP), 8 pockets (best druggability 0.75). MolNFT v1 #9797 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1I7L
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synapsin II
- UniProt
- Q63537
- Ligands
- ATP
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Synapsin II | protein | 309 | 28% helix, 32% strand | Q63537 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.75 | 0.96 | 34 | empty |
| 2 | 341 | 0.74 | 0.85 | 42 | ATP |
| 3 | 97 | 0.74 | 0.95 | 32 | empty |
| 4 | 492 | 0.72 | 0.81 | 60 | ATP |
| 5 | 406 | 0.58 | 0.75 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 1887 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1I7L · Crystal structure analysis of the complex of the C domain of synapsin II from rat with ATP · the same entry in another collection · chain A against A, TM-score 1.00
- Q63537 · AlphaFold monomer V2.0 prediction for synapsin-2 (Q63537) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q63537
- Elsewhere: RCSB PDB 1I7L · PDBe 1I7L · UniProt Q63537
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