Research workbench
Cryo-EM structure of human CALHM5 in the presence of edta
Analyse Cryo-EM structure of human CALHM5 in the presence of edta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D61
- Type
- protein
- Length
- 3,168 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium homeostasis modulator protein 5
- UniProt
- Q8N5C1
- Ligands
- PA8
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K | Calcium homeostasis modulator protein 5 | protein | 288 | 65% helix, 0% strand | Q8N5C1 |
Ligands and binding sites
- PA8 · 1,2-dioctanoyl-sn-glycero-3-phosphate · ligand · 55 copies · chains A, B, K, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.80 | 0.81 | 103 | PA8 |
| 2 | 768 | 0.79 | 0.82 | 61 | PA8 |
| 3 | 604 | 0.78 | 0.83 | 49 | empty |
| 4 | 453 | 0.77 | 0.85 | 47 | empty |
| 5 | 599 | 0.77 | 0.83 | 51 | empty |
Interfaces
22 interfaces between chains.
- H–I · 2685 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 2679 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 2678 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2675 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 2673 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide (disulfide).
Compared structures
- 7D61 · Cryo-EM Structure of human CALHM5 in the presence of EDTA · the same entry in another collection · chain K against K, TM-score 1.00
- Q8N5C1 · AlphaFold monomer V2.0 prediction for calcium homeostasis modulator protein 5 (Q8N5C1) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 Q8N5C1
- Elsewhere: RCSB PDB 7D61 · PDBe 7D61 · UniProt Q8N5C1
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