Research workbench
Cryo-EM structure of ATP13A2 in the alf-bound E2-pi-like state
Analyse Cryo-EM structure of ATP13A2 in the alf-bound E2-pi-like state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N72
- Type
- protein
- Length
- 1,030 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, PC1, ALF, SPM, MG
- Pockets
- 13 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 3 of polyamine-transporting ATPase 13A2 (EC 7.6.2.-) | protein | 1030 | 46% helix, 21% strand | Q9NQ11 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 3 copies · chains A
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- SPM · Spermine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.75 | 0.77 | 148 | MG |
| 2 | 587 | 0.68 | 0.77 | 48 | PC1 |
| 3 | 368 | 0.65 | 0.80 | 60 | empty |
| 4 | 101 | 0.62 | 0.88 | 29 | SPM |
| 5 | 212 | 0.56 | 0.79 | 27 | empty |
Compared structures
- 7N72 · Cryo-EM structure of ATP13A2 in the AlF-bound E2-Pi-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 0.83
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 7N72 · PDBe 7N72 · UniProt Q9NQ11
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