Research workbench
Cryo-EM structure of the human ATP13A2 (spm-bound E2P state)
Analyse Cryo-EM structure of the human ATP13A2 (spm-bound E2P state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VPK
- Type
- protein
- Length
- 1,055 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
- BEF, SPM, NAG, MG
- Pockets
- 16 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyamine-transporting ATPase 13A2 (EC 7.6.2.-) | protein | 1055 | 44% helix, 17% strand | Q9NQ11 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A
- SPM · Spermine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.75 | 0.77 | 90 | empty |
| 2 | 776 | 0.70 | 0.76 | 73 | empty |
| 3 | 574 | 0.68 | 0.78 | 49 | empty |
| 4 | 204 | 0.64 | 0.83 | 35 | empty |
| 5 | 126 | 0.60 | 0.85 | 30 | SPM |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 7VPK · Cryo-EM structure of the human ATP13A2 (SPM-bound E2P 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 0.82
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 7VPK · PDBe 7VPK · UniProt Q9NQ11
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