MolNFT v1 · #55561 · protein
Synaptotagmin-1 C2B domain with phosphoserine
2YOA: “Synaptotagmin-1 C2B domain with phosphoserine”. X-ray diffraction, 3 ligands (SEP, CA, SCN), 1 pocket (best druggability 0.53). MolNFT v1 #55561 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YOA
- Type
- protein
- Length
- 298 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptotagmin-1
- UniProt
- P21707
- Ligands
- SEP, CA, SCN
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Synaptotagmin-1 | protein | 149 | 18% helix, 46% strand | P21707 |
| B | Synaptotagmin-1 | protein | 149 | 19% helix, 46% strand | P21707 |
Ligands and binding sites
- SEP · Phosphoserine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 7 copies · chains A, B
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.53 | 0.79 | 29 | SCN |
Interfaces
1 interface between chains.
- A–B · 336 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P21707
- Elsewhere: RCSB PDB 2YOA · PDBe 2YOA · UniProt P21707
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