Research workbench
Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the autoinhibited state (pH 7.4, C1 symmetry)
Analyse Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VH5
- Type
- protein
- Length
- 4,824 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasma membrane ATPase 1
- EC
- 7.1.2.1
- UniProt
- P05030
- Ligands
- POV, SPH
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Plasma membrane ATPase 1 (EC 7.1.2.1) | protein | 804 | 53% helix, 14% strand | P05030 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 51 copies · chains A, F, B, C, D, E
- SPH · Sphingosine · ligand
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.74 | 0.77 | 88 | empty |
| 2 | 913 | 0.73 | 0.77 | 86 | empty |
| 3 | 932 | 0.73 | 0.77 | 82 | empty |
| 4 | 850 | 0.73 | 0.77 | 81 | empty |
| 5 | 847 | 0.73 | 0.77 | 79 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1279 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1262 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1251 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1246 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 1244 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7VH5 · Cryo-EM structure of the hexameric plasma membrane H+-ATPase in the autoinhibited state… · the same entry in another collection · chain C against C, TM-score 1.00
- P05030 · AlphaFold monomer V2.0 prediction for plasma membrane ATPase 1 (P05030) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 P05030
- Elsewhere: RCSB PDB 7VH5 · PDBe 7VH5 · UniProt P05030
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