MolNFT v1 · #181781 · protein
Human ATP13A2 in the amppnp-bound occluded state
7M5V · Polyamine-transporting ATPase 13A2: “Human ATP13A2 in the amppnp-bound occluded state”. Electron microscopy, 8 ligands (D10, 1DO, Y01), 20 pockets (best druggability 0.81). MolNFT v1 #181781 on GenesisL1: 3D structure, binding sites…
- PDB
- 7M5V
- Type
- protein
- Length
- 1,046 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyamine-transporting ATPase 13A2
- EC
- 7.6.2.-
- UniProt
- Q9NQ11
- Ligands
- D10, 1DO, Y01, D12, ANP, EUJ, NAG, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine-transporting ATPase 13A2 (EC 7.6.2.-) | protein | 1046 | 44% helix, 18% strand | Q9NQ11 |
Ligands and binding sites
- D10 · Decane · ligand · 9 copies · chains A
- 1DO · 1-dodecanol · ligand · 4 copies · chains A
- Y01 · Cholesterol hemisuccinate · ligand · 4 copies · chains A
- D12 · Dodecane · ligand · 2 copies · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- EUJ · (2R)-3-{[(S)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,4,6-trihydroxy-3,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- MG · Magnesium ion · metal · chains A
- LMT · Dodecyl-beta-D-maltoside · additive · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.81 | 0.84 | 80 | MG, ANP |
| 2 | 54 | 0.70 | 0.97 | 18 | empty |
| 3 | 439 | 0.66 | 0.78 | 40 | empty |
| 4 | 434 | 0.63 | 0.76 | 40 | 1DO, LMT |
| 5 | 290 | 0.56 | 0.77 | 29 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
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 7M5V · PDBe 7M5V · UniProt Q9NQ11
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