Research workbench
Extended-synaptotagmin 2, C2A- and C2B-domains
Analyse Extended-synaptotagmin 2, C2A- and C2B-domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NPJ
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extended synaptotagmin-2
- UniProt
- A0FGR8
- Ligands
- NA, CL
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extended synaptotagmin-2 | protein | 292 | 8% helix, 47% strand | A0FGR8 |
| B | Extended synaptotagmin-2 | protein | 282 | 9% helix, 49% strand | A0FGR8 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.78 | 0.80 | 86 | CL, ACT |
| 2 | 427 | 0.64 | 0.77 | 47 | CL |
| 3 | 303 | 0.59 | 0.77 | 31 | ACT |
| 4 | 66 | 0.44 | 0.82 | 16 | empty |
| 5 | 54 | 0.42 | 0.83 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1871 Ų buried · 15 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 A0FGR8
- Elsewhere: RCSB PDB 4NPJ · PDBe 4NPJ · UniProt A0FGR8
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