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
- 5HCA
- Type
- protein
- Length
- 795 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALRETICULIN,CALRETICULIN
- UniProt
- F2VN92
- Ligands
- BGC, CA, SO4, CL, NH4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | CALRETICULIN,CALRETICULIN | protein | 265 | 13% helix, 43% strand | F2VN92 |
| A | CALRETICULIN,CALRETICULIN | protein | 266 | 15% helix, 41% strand | F2VN92 |
| B | CALRETICULIN,CALRETICULIN | protein | 264 | 14% helix, 41% strand | F2VN92 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · chains C, A
- CA · Calcium ion · metal · 3 copies · chains C, A, B
- SO4 · Sulfate ion · ion · 5 copies · chains C, A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · chains A
- ACT · Acetate ion · additive · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.77 | 0.80 | 89 | CL |
| 2 | 164 | 0.68 | 0.88 | 36 | BGC |
| 3 | 67 | 0.65 | 0.93 | 23 | empty |
| 4 | 67 | 0.35 | 0.77 | 19 | empty |
| 5 | 77 | 0.33 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1012 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 955 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5HCA · Globular Domain of the Entamoeba histolytica calreticulin in complex with glucose · the same entry in another collection · chain C against C, 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 5HCA · PDBe 5HCA · UniProt F2VN92
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