Research workbench
Crystal structure of the globular domain of human calreticulin mutant D71K
Analyse Crystal structure of the globular domain of human calreticulin mutant D71K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LK5
- Type
- protein
- Length
- 2,536 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALRETICULIN,CALRETICULIN
- UniProt
- P27797
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | CALRETICULIN,CALRETICULIN | protein | 256 | 17% helix, 42% strand | P27797 |
| B | CALRETICULIN,CALRETICULIN | protein | 251 | 17% helix, 43% strand | P27797 |
| C, F, G, J | CALRETICULIN,CALRETICULIN | protein | 255 | 17% helix, 42% strand | P27797 |
| E | CALRETICULIN,CALRETICULIN | protein | 249 | 17% helix, 42% strand | P27797 |
| H | CALRETICULIN,CALRETICULIN | protein | 254 | 17% helix, 42% strand | P27797 |
| I | CALRETICULIN,CALRETICULIN | protein | 250 | 17% helix, 42% strand | P27797 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CL · Chloride ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.72 | 0.77 | 77 | empty |
| 2 | 619 | 0.72 | 0.80 | 82 | empty |
| 3 | 530 | 0.71 | 0.80 | 66 | empty |
| 4 | 500 | 0.67 | 0.78 | 43 | empty |
| 5 | 435 | 0.64 | 0.78 | 43 | empty |
Interfaces
17 interfaces between chains.
- C–F · 568 Ų buried · 4 hydrogen bonds · protein-protein
- G–J · 558 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 493 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 383 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 363 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
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 P27797
- Elsewhere: RCSB PDB 5LK5 · PDBe 5LK5 · UniProt P27797
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