Research workbench
Cryo-EM structure of the killifish CALHM1
Analyse Cryo-EM structure of the killifish CALHM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LMT
- Type
- protein
- Length
- 2,032 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.66
- Source
- Oryzias latipes
- Molecule
- Calcium homeostasis modulator 1
- UniProt
- H2MCM1
- Ligands
- Y01
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 2.66 · 1 distinct chain · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Calcium homeostasis modulator 1 | protein | 254 | 76% helix, 0% strand | H2MCM1 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 32 copies · chains A, B, H, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.83 | 0.83 | 87 | Y01 |
| 2 | 1108 | 0.83 | 0.83 | 85 | Y01 |
| 3 | 1168 | 0.83 | 0.83 | 87 | Y01 |
| 4 | 1194 | 0.83 | 0.83 | 84 | Y01 |
| 5 | 664 | 0.79 | 0.83 | 50 | Y01 |
Interfaces
16 interfaces between chains.
- C–D · 2431 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 2425 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2419 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 2416 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 2415 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6LMT · Cryo-EM structure of the killifish CALHM1 · 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 H2MCM1
- Elsewhere: RCSB PDB 6LMT · PDBe 6LMT · UniProt H2MCM1
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