Research workbench
Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50B in the auto-inhibited E2P state
Analyse Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50B in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VGH
- Type
- protein
- Length
- 1,521 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell cycle control protein 50B; Phospholipid-transporting ATPase ic
- EC
- 7.6.2.1
- UniProt
- Q3MIR4, O43520
- Ligands
- NAG, MAN, MG
- Pockets
- 18 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 35% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell cycle control protein 50B | protein | 338 | 26% helix, 15% strand | Q3MIR4 |
| B | Phospholipid-transporting ATPase ic (EC 7.6.2.1) | protein | 1183 | 37% helix, 12% strand | O43520 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, A
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.82 | 0.83 | 87 | empty |
| 2 | 492 | 0.80 | 0.87 | 65 | empty |
| 3 | 979 | 0.76 | 0.78 | 74 | empty |
| 4 | 950 | 0.73 | 0.77 | 122 | empty |
| 5 | 419 | 0.67 | 0.79 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 4029 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 3 disulfide, 1 modified (N-glycosylation, disulfide, phosphorylation).
Compared structures
- 7VGH · Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50B 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 0.92
- Q3MIR4 · AlphaFold monomer V2.0 prediction for cell cycle control protein 50B (Q3MIR4) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q3MIR4
- Every structure of UniProt O43520
- Elsewhere: RCSB PDB 7VGH · PDBe 7VGH · UniProt Q3MIR4 · UniProt O43520
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