MolNFT v1 · #117712 · protein
Structure of a trimeric intracellular cation channel from C. elegans with bound CA2+
5EGI · Uncharacterized protein Y57A10A.10: “Structure of a trimeric intracellular cation channel from C. elegans with bound CA2+”. X-ray diffraction, 2 ligands (PT5, CA), 9 pockets (best druggability 0.84). MolNFT v1 #117712 on GenesisL1…
- PDB
- 5EGI
- Type
- protein
- Length
- 697 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein Y57A10A.10
- UniProt
- Q9NA75
- Ligands
- PT5, CA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein Y57A10A.10 | protein | 232 | 79% helix, 0% strand | Q9NA75 |
| B | Uncharacterized protein Y57A10A.10 | protein | 233 | 80% helix, 0% strand | Q9NA75 |
Ligands and binding sites
- PT5 · (1S)-2-{[(R)-hydroxy{[(1r,2r,3s,4r,5r,6s)-2,3,6-trihydroxy-4,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy) methyl]ethyl (8E,11E)-icosa-5,8,11,14-tetraenoate · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal
- DMU · Decyl-beta-D-maltopyranoside · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.84 | 0.88 | 65 | PT5 |
| 2 | 180 | 0.76 | 0.92 | 37 | empty |
| 3 | 213 | 0.74 | 0.89 | 40 | empty |
| 4 | 250 | 0.74 | 0.88 | 40 | empty |
| 5 | 53 | 0.57 | 0.91 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 758 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 742 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 725 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5EGI · Structure of a Trimeric Intracellular Cation channel from C. elegans with bound Ca2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NA75 · AlphaFold monomer V2.0 prediction for trimeric intracellular cation channel type 1B.1… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9NA75
- Elsewhere: RCSB PDB 5EGI · PDBe 5EGI · UniProt Q9NA75
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