Research workbench
Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50A in the auto-inhibited E2PI-ps 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
- 7VGJ
- Type
- protein
- Length
- 1,414 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipid-transporting ATPase ic; Cell cycle control protein 50A
- EC
- 7.6.2.1
- UniProt
- O43520, Q9NV96
- Ligands
- P5S
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase ic (EC 7.6.2.1) | protein | 1084 | 41% helix, 11% strand | O43520 |
| B | Cell cycle control protein 50A | protein | 330 | 28% helix, 16% strand | Q9NV96 |
Ligands and binding sites
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.85 | 0.86 | 77 | empty |
| 2 | 1197 | 0.79 | 0.81 | 107 | P5S |
| 3 | 212 | 0.76 | 0.91 | 37 | empty |
| 4 | 1148 | 0.74 | 0.77 | 84 | empty |
| 5 | 106 | 0.74 | 0.94 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 3529 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7VGJ · Cryo-EM structure of the human P4-type flippase ATP8B1-CDC50A in the auto-inhibited… · 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 A against A, TM-score 0.92
- Q9NV96 · AlphaFold monomer V2.0 prediction for cell cycle control protein 50A (Q9NV96) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 O43520
- Every structure of UniProt Q9NV96
- Elsewhere: RCSB PDB 7VGJ · PDBe 7VGJ · UniProt O43520 · UniProt Q9NV96
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