Research workbench
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 zero Ca2+
Analyse Structural mechanisms of extracellular ion exchange and induced binding-site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HWX
- Type
- protein
- Length
- 294 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045…
- Molecule
- sodium,calcium exchanger
- UniProt
- Q57556
- Ligands
- MYS, NA, CL
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 83% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | sodium,calcium exchanger | protein | 294 | 83% helix, 1% strand | Q57556 |
Ligands and binding sites
- MYS · Pentadecane · ligand · 5 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.61 | 0.77 | 35 | empty |
Compared structures
- 5HWX · 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 5HWX · PDBe 5HWX · UniProt Q57556
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