Research workbench
Native bovine skeletal calsequestrin, low-CA2+ form
Analyse Native bovine skeletal calsequestrin, low-CA2+ form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KN0
- Type
- protein
- Length
- 1,383 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calsequestrin
- UniProt
- Q05JF3
- Ligands
- NAG, BMA, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Calsequestrin | protein | 346 | 38% helix, 19% strand | Q05JF3 |
| C | Calsequestrin | protein | 345 | 39% helix, 19% strand | Q05JF3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D, A, C
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 19 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.84 | 0.87 | 84 | MPD |
| 2 | 651 | 0.83 | 0.87 | 74 | MPD |
| 3 | 461 | 0.72 | 0.82 | 41 | empty |
| 4 | 462 | 0.71 | 0.81 | 43 | empty |
| 5 | 251 | 0.68 | 0.84 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2697 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2606 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 718 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 5KN0 · Native bovine skeletal calsequestrin, low-Ca2+ form · the same entry in another collection · chain A against A, TM-score 1.00
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 Q05JF3
- Elsewhere: RCSB PDB 5KN0 · PDBe 5KN0 · UniProt Q05JF3
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