MolNFT v1 · #66333 · protein
Crystal structure of synaptotagmin
3HN8 · Synaptotagmin-3: “Crystal structure of synaptotagmin”. X-ray diffraction, 2 ligands (CA, ZN), 16 pockets (best druggability 0.70). MolNFT v1 #66333 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HN8
- Type
- protein
- Length
- 837 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptotagmin-3
- UniProt
- P40748
- Ligands
- CA, ZN
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Synaptotagmin-3 | protein | 279 | 8% helix, 44% strand | P40748 |
Ligands and binding sites
- CA · Calcium ion · metal · 18 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.70 | 0.76 | 58 | empty |
| 2 | 74 | 0.49 | 0.84 | 18 | empty |
| 3 | 135 | 0.49 | 0.79 | 22 | empty |
| 4 | 83 | 0.48 | 0.82 | 21 | empty |
| 5 | 74 | 0.48 | 0.83 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 584 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 556 Ų buried · 10 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 P40748
- Elsewhere: RCSB PDB 3HN8 · PDBe 3HN8 · UniProt P40748
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