Research workbench
Calmodulin N53I variant bound to cardiac ryanodine receptor (RYR2) calmodulin binding domain
Analyse Calmodulin N53I variant bound to cardiac ryanodine receptor (RYR2) calmodulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y4P
- Type
- protein
- Length
- 164 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-1; Ryanodine receptor 2
- UniProt
- P0DP23, E9Q401
- Ligands
- CA
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-1 | protein | 139 | 60% helix, 6% strand | P0DP23 |
| B | Ryanodine receptor 2 | protein | 25 | 88% helix, 0% strand | E9Q401 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A
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 | 92 | 0.56 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1590 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6Y4P · Calmodulin N53I variant bound to cardiac ryanodine receptor (RyR2) calmodulin binding… · the same entry in another collection · chain A against A, TM-score 1.00
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain A against A, TM-score 0.51
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 P0DP23
- Every structure of UniProt E9Q401
- Elsewhere: RCSB PDB 6Y4P · PDBe 6Y4P · UniProt P0DP23 · UniProt E9Q401
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