Research workbench
Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50A in the auto-inhibited E2P state
Analyse Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50A in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VGI
- Type
- protein
- Length
- 1,493 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell cycle control protein 50A; Phospholipid-transporting ATPase ic
- EC
- 7.6.2.1
- UniProt
- Q9NV96, O43520
- Ligands
- NAG, MAN, MG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell cycle control protein 50A | protein | 331 | 27% helix, 19% strand | Q9NV96 |
| B | Phospholipid-transporting ATPase ic (EC 7.6.2.1) | protein | 1162 | 34% helix, 13% strand | O43520 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · chains A
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.78 | 0.88 | 62 | empty |
| 2 | 196 | 0.78 | 0.93 | 33 | empty |
| 3 | 994 | 0.77 | 0.79 | 80 | empty |
| 4 | 752 | 0.74 | 0.79 | 57 | empty |
| 5 | 738 | 0.70 | 0.77 | 95 | empty |
Interfaces
1 interface between chains.
- A–B · 3900 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 1 disulfide, 1 modified (N-glycosylation, disulfide, phosphorylation).
Compared structures
- 7VGI · Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50A in the auto-inhibited E2P… · the same entry in another collection · chain A against A, TM-score 1.00
- O43520 · AlphaFold monomer V2.0 prediction for phospholipid-transporting ATPase ic (O43520) · a predicted model of the same protein · chain B against A, TM-score 0.93
- Q9NV96 · AlphaFold monomer V2.0 prediction for cell cycle control protein 50A (Q9NV96) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q9NV96
- Every structure of UniProt O43520
- Elsewhere: RCSB PDB 7VGI · PDBe 7VGI · UniProt Q9NV96 · UniProt O43520
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