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Crystal structure of a human cardiac calsequestrin filament complexed with ytterbium
Analyse Crystal structure of a human cardiac calsequestrin filament complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OWW
- Type
- protein
- Length
- 2,632 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calsequestrin-2
- UniProt
- O14958
- Ligands
- YB, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Calsequestrin-2 | protein | 329 | 35% helix, 20% strand | O14958 |
Ligands and binding sites
- YB · Ytterbium (III) ion · metal · 63 copies · chains A, B, E, H, C, D, G, F
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, E, D, G, F, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.88 | 0.90 | 138 | SO4, YB |
| 2 | 1073 | 0.87 | 0.89 | 117 | YB, SO4 |
| 3 | 681 | 0.86 | 0.91 | 88 | YB, SO4 |
| 4 | 279 | 0.77 | 0.89 | 41 | empty |
| 5 | 506 | 0.77 | 0.84 | 53 | YB |
Interfaces
16 interfaces between chains.
- C–H · 2835 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 2834 Ų buried · 34 hydrogen bonds · protein-protein
- D–G · 2823 Ų buried · 28 hydrogen bonds · protein-protein
- C–E · 872 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 862 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6OWW · Crystal structure of a Human Cardiac Calsequestrin Filament Complexed with Ytterbium · the same entry in another collection · chain H against H, TM-score 1.00
- O14958 · AlphaFold monomer V2.0 prediction for calsequestrin-2 (O14958) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 O14958
- Elsewhere: RCSB PDB 6OWW · PDBe 6OWW · UniProt O14958
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