MolNFT v1 · #123227 · protein
Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_MJ soaked with 2.5 mm na+ and 1MM SR2+
5JDL · Uncharacterized membrane protein MJ0091: “Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium…”. X-ray diffraction, 3 ligands (MYS, SR, CL), 2 pockets (best druggability…
- PDB
- 5JDL
- Type
- protein
- Length
- 299 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized membrane protein MJ0091
- UniProt
- Q57556
- Ligands
- MYS, SR, CL
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized membrane protein MJ0091 | protein | 299 | 76% helix, 2% strand | Q57556 |
Ligands and binding sites
- MYS · Pentadecane · ligand · 3 copies · chains A
- SR · Strontium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 4 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.59 | 0.76 | 32 | empty |
| 2 | 92 | 0.39 | 0.76 | 14 | empty |
Compared structures
- 5JDL · Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q57556 · AlphaFold monomer V2.0 prediction for uncharacterized membrane protein MJ0091 (Q57556) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q57556
- Elsewhere: RCSB PDB 5JDL · PDBe 5JDL · UniProt Q57556
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