MolNFT v1 · #121529 · protein
Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium EXCHANGERNCX_MJ soaked with 150 mm na+ and nominal CA2+
5HYA · SODIUM,CALCIUM exchanger: “Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium…”. X-ray diffraction, 3 ligands (MYS, NA, CA), 3 pockets (best druggability 0.60). MolNFT v1…
- PDB
- 5HYA
- Type
- protein
- Length
- 297 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM,CALCIUM exchanger
- UniProt
- Q57556
- Ligands
- MYS, NA, CA
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SODIUM,CALCIUM exchanger | protein | 297 | 82% helix, 2% strand | Q57556 |
Ligands and binding sites
- MYS · Pentadecane · ligand · 9 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A
- ACT · Acetate ion · 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.60 | 0.82 | 25 | OLC |
| 2 | 235 | 0.50 | 0.74 | 31 | ACT, OLC |
| 3 | 57 | 0.38 | 0.79 | 13 | empty |
Compared structures
- 5HYA · 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 0.98
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 Q57556
- Elsewhere: RCSB PDB 5HYA · PDBe 5HYA · UniProt Q57556
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