MolNFT v1 · #123232 · protein
Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_MJ soaked with 100 mm na+ and 10MM SR2+
5JDQ · Uncharacterized membrane protein MJ0091: “Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium…”. X-ray diffraction, 4 ligands (MYS, NA, SR), 3 pockets (best druggability…
- PDB
- 5JDQ
- Type
- protein
- Length
- 296 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized membrane protein MJ0091
- UniProt
- Q57556
- Ligands
- MYS, NA, SR, CL
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized membrane protein MJ0091 | protein | 296 | 82% helix, 2% strand | Q57556 |
Ligands and binding sites
- MYS · Pentadecane · ligand · 5 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- SR · Strontium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.59 | 0.79 | 26 | empty |
| 2 | 249 | 0.50 | 0.74 | 31 | OLC |
| 3 | 64 | 0.38 | 0.78 | 13 | empty |
Compared structures
- 5JDQ · 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 5JDQ · PDBe 5JDQ · UniProt Q57556
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