MolNFT v1 · #121501 · protein
Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_MJ soaked with zero na+ and CA2+
5HXH · SODIUM,CALCIUM exchanger: “Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium…”. X-ray diffraction, 2 ligands (MYS, CA), 6 pockets (best druggability 0.60). MolNFT v1 #121501…
- PDB
- 5HXH
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SODIUM,CALCIUM exchanger
- UniProt
- Q57556
- Ligands
- MYS, CA
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SODIUM,CALCIUM exchanger | protein | 293 | 80% helix, 1% strand | Q57556 |
| B | SODIUM,CALCIUM exchanger | protein | 291 | 78% helix, 2% strand | Q57556 |
Ligands and binding sites
- MYS · Pentadecane · ligand · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.60 | 0.77 | 39 | empty |
| 2 | 351 | 0.59 | 0.75 | 28 | OLC |
| 3 | 300 | 0.52 | 0.73 | 30 | 1PE |
| 4 | 155 | 0.46 | 0.76 | 20 | empty |
| 5 | 77 | 0.39 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 384 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HXH · 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 B 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 5HXH · PDBe 5HXH · UniProt Q57556
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