Research workbench
Globular domain of the entamoeba histolytica calreticulin in complex with glucose
Analyse Globular domain of the entamoeba histolytica calreticulin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HCB
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calreticulin
- UniProt
- F2VN92
- Ligands
- CA, SO4, CL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Calreticulin | protein | 265 | 12% helix, 40% strand | F2VN92 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.72 | 0.92 | 35 | empty |
| 2 | 52 | 0.44 | 0.84 | 17 | empty |
| 3 | 79 | 0.41 | 0.79 | 21 | empty |
| 4 | 70 | 0.34 | 0.76 | 16 | empty |
| 5 | 57 | 0.28 | 0.74 | 16 | GOL |
Interfaces
1 interface between chains.
- A–B · 1792 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5HCB · Globular Domain of the Entamoeba histolytica calreticulin in complex with glucose · 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 F2VN92
- Elsewhere: RCSB PDB 5HCB · PDBe 5HCB · UniProt F2VN92
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