Research workbench
Voltage-gated sodium channel 1.2 C-terminal domain in complex with FGF13U and CA2+/CALMODULIN
Analyse Voltage-gated sodium channel 1.2 C-terminal domain in complex with FGF13U and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JPZ
- Type
- protein
- Length
- 866 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibroblast growth factor 13; Sodium channel protein type 2 subunit alpha; Calmodulin
- UniProt
- Q92913, Q99250, P62158
- Ligands
- CA
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Fibroblast growth factor 13 | protein | 148 | 8% helix, 50% strand | Q92913 |
| B, H | Sodium channel protein type 2 subunit alpha | protein | 142 | 57% helix, 8% strand | Q99250 |
| C, I | Calmodulin | protein | 143 | 54% helix, 6% strand | P62158 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.62 | 0.78 | 35 | empty |
| 2 | 356 | 0.61 | 0.77 | 39 | empty |
| 3 | 482 | 0.61 | 0.75 | 68 | empty |
| 4 | 229 | 0.54 | 0.77 | 22 | empty |
| 5 | 314 | 0.54 | 0.74 | 48 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1765 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 1747 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1099 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 1091 Ų buried · 16 hydrogen bonds · protein-protein
- A–I · 194 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JPZ · Voltage-gated sodium channel 1.2 C-terminal domain in complex with FGF13U and… · the same entry in another collection · chain I against I, TM-score 1.00
- Q92913 · AlphaFold monomer V2.0 prediction for fibroblast growth factor 13 (Q92913) · a predicted model of the same protein · chain E against A, TM-score 0.99
- Q99250 · AlphaFold monomer V2.0 prediction for sodium channel protein type 2 subunit alpha (Q99250) · a predicted model of the same protein · chain B against A, TM-score 0.72
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 Q92913
- Every structure of UniProt Q99250
- Every structure of UniProt P62158
- Elsewhere: RCSB PDB 4JPZ · PDBe 4JPZ · UniProt Q92913 · UniProt Q99250 · UniProt P62158
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