Research workbench
Cryo-EM structure of ATP13A2 in the ADP-alf-bound E1P-ADP-like state
Analyse Cryo-EM structure of ATP13A2 in the ADP-alf-bound E1P-ADP-like state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N73
- Type
- protein
- Length
- 1,036 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 3 of polyamine-transporting ATPase 13A2
- EC
- 7.6.2.-
- UniProt
- Q9NQ11
- Ligands
- Y01, ADP, ALF, MG
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 3 of polyamine-transporting ATPase 13A2 (EC 7.6.2.-) | protein | 1036 | 46% helix, 18% strand | Q9NQ11 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.80 | 0.82 | 73 | ADP, ALF, MG |
| 2 | 261 | 0.61 | 0.80 | 32 | empty |
| 3 | 226 | 0.59 | 0.80 | 38 | empty |
| 4 | 213 | 0.57 | 0.80 | 31 | empty |
| 5 | 79 | 0.57 | 0.87 | 16 | empty |
Compared structures
- 7N73 · Cryo-EM structure of ATP13A2 in the ADP-AlF-bound E1P-ADP-like state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQ11 · AlphaFold monomer V2.0 prediction for polyamine-transporting ATPase 13A2 (Q9NQ11) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9NQ11
- Elsewhere: RCSB PDB 7N73 · PDBe 7N73 · UniProt Q9NQ11
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