Research workbench
Structure of a trimeric intracellular cation channel from C. elegans in the absence of CA2+
Analyse Structure of a trimeric intracellular cation channel from C. elegans in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EIK
- Type
- protein
- Length
- 234 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein Y57A10A.28
- UniProt
- Q9NA73
- Ligands
- PT5, CPL, MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein Y57A10A.28 | protein | 234 | 77% helix, 0% strand | Q9NA73 |
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 · chains A
- CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ACT · Acetate ion · additive · 5 copies · chains A
- DMU · Decyl-beta-D-maltopyranoside · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.66 | 0.78 | 46 | ACT |
| 2 | 199 | 0.50 | 0.76 | 21 | empty |
| 3 | 50 | 0.30 | 0.76 | 12 | empty |
| 4 | 51 | 0.29 | 0.75 | 10 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5EIK · Structure of a Trimeric Intracellular Cation channel from C. elegans in the absence of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NA73 · AlphaFold monomer V2.0 prediction for trimeric intracellular cation channel type 1B.2… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9NA73
- Elsewhere: RCSB PDB 5EIK · PDBe 5EIK · UniProt Q9NA73
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