MolNFT v1 · #124707 · protein
Native bovine skeletal calsequestrin, high-CA2+ form
5KN2: “Native bovine skeletal calsequestrin, high-CA2+ form”. X-ray diffraction, 2 ligands (NAG, CA), 18 pockets (best druggability 0.84). MolNFT v1 #124707 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KN2
- Type
- protein
- Length
- 1,055 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calsequestrin
- UniProt
- Q05JF3
- Ligands
- NAG, CA
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calsequestrin | protein | 352 | 39% helix, 20% strand | Q05JF3 |
| B | Calsequestrin | protein | 351 | 39% helix, 20% strand | Q05JF3 |
| C | Calsequestrin | protein | 352 | 40% helix, 20% strand | Q05JF3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- CA · Calcium ion · metal · 39 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.84 | 0.85 | 101 | CA |
| 2 | 1033 | 0.77 | 0.79 | 67 | empty |
| 3 | 336 | 0.72 | 0.85 | 28 | empty |
| 4 | 420 | 0.70 | 0.82 | 33 | empty |
| 5 | 350 | 0.70 | 0.83 | 27 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2407 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 163 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 5KN2 · Native bovine skeletal calsequestrin, high-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 5KN2 · PDBe 5KN2 · UniProt Q05JF3
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