Research workbench
Cryo-EM structure of the calcium homeostasis modulator 1 channel
Analyse Cryo-EM structure of the calcium homeostasis modulator 1 channel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LYG
- Type
- protein
- Length
- 1,856 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium homeostasis modulator 1
- UniProt
- E7F2J4
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Calcium homeostasis modulator 1 | protein | 232 | 70% helix, 1% strand | E7F2J4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.75 | 0.80 | 58 | empty |
| 2 | 539 | 0.75 | 0.82 | 40 | empty |
| 3 | 678 | 0.75 | 0.80 | 47 | empty |
| 4 | 545 | 0.75 | 0.82 | 47 | empty |
| 5 | 542 | 0.75 | 0.82 | 47 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1823 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 1823 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1822 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1820 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 1819 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6LYG · Cryo-EM structure of the calcium homeostasis modulator 1 channel · 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 E7F2J4
- Elsewhere: RCSB PDB 6LYG · PDBe 6LYG · UniProt E7F2J4
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