Research workbench
Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain
Analyse Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CCJ
- Type
- protein
- Length
- 599 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synaptotagmin-1
- UniProt
- P21707
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Synaptotagmin-1 | protein | 148 | 18% helix, 47% strand | P21707 |
| B | Synaptotagmin-1 | protein | 151 | 15% helix, 46% strand | P21707 |
| D | Synaptotagmin-1 | protein | 152 | 15% helix, 45% strand | P21707 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 22 copies · chains A, C, D, B
- GOL · Glycerol · additive · 27 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.72 | 0.80 | 71 | GOL, SO4 |
| 2 | 323 | 0.64 | 0.79 | 38 | GOL |
| 3 | 99 | 0.63 | 0.88 | 21 | GOL |
| 4 | 60 | 0.39 | 0.80 | 15 | empty |
| 5 | 62 | 0.31 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 773 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 754 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 622 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 243 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 101 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CCJ · Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain · the same entry in another collection · chain A against A, TM-score 1.00
- P21707 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21707) · 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 P21707
- Elsewhere: RCSB PDB 5CCJ · PDBe 5CCJ · UniProt P21707
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