MolNFT v1 · #113902 · protein
Kinetics by X-ray crystallography: tl+-substitution of bound K+ in the E2.MGF42-.2K+ crystal after 55 min
5AVZ · Na, K-ATPase alpha subunit: “Kinetics by X-ray crystallography: tl+-substitution of bound K+ in the E2.MGF42-.2K+ crystal after 55 min”. X-ray diffraction, 6 ligands (MF4, CLR, NAG), 20 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5AVZ
- Type
- protein
- Length
- 1,299 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Na, K-ATPase alpha subunit; NA+,K+-ATPase beta subunit; Phospholemman-like protein
- UniProt
- Q4H132, C4IX13, Q70Q12
- Ligands
- MF4, CLR, NAG, TL, MG, K
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Na, K-ATPase alpha subunit | protein | 992 | 49% helix, 15% strand | Q4H132 |
| B | NA+,K+-ATPase beta subunit | protein | 268 | 22% helix, 18% strand | C4IX13 |
| G | Phospholemman-like protein | protein | 39 | 69% helix, 0% strand | Q70Q12 |
Ligands and binding sites
- MF4 · Tetrafluoromagnesate(2-) · ligand · chains A
- CLR · Cholesterol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
- TL · Thallium (I) ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · chains A
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.77 | 0.79 | 70 | empty |
| 2 | 597 | 0.73 | 0.81 | 71 | K, TL |
| 3 | 668 | 0.70 | 0.78 | 83 | empty |
| 4 | 51 | 0.69 | 0.97 | 13 | empty |
| 5 | 344 | 0.61 | 0.78 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2122 Ų buried · 28 hydrogen bonds · protein-protein
- A–G · 786 Ų buried · 1 hydrogen bond · protein-protein
- B–G · 514 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5AVZ · Kinetics by X-ray crystallography: Tl+-substitution of bound K+ in the E2.MgF42-.2K+… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q4H132
- Every structure of UniProt C4IX13
- Every structure of UniProt Q70Q12
- Elsewhere: RCSB PDB 5AVZ · PDBe 5AVZ · UniProt Q4H132 · UniProt C4IX13 · UniProt Q70Q12
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