MolNFT v1 · #174352 · protein
Cryo-EM structure of a human ATP11C-CDC50A flippase in E1-amppcp state
7BSP: “Cryo-EM structure of a human ATP11C-CDC50A flippase in E1-amppcp state”. Electron microscopy, 2 ligands (ACP, NAG), 14 pockets (best druggability 0.84). MolNFT v1 #174352 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7BSP
- Type
- protein
- Length
- 1,352 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP11C; CDC50A
- Ligands
- ACP, NAG
- Pockets
- 14 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP11C | protein | 1028 | 40% helix, 12% strand | — |
| C | CDC50A | protein | 324 | 27% helix, 15% strand | — |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.84 | 0.86 | 101 | ACP |
| 2 | 595 | 0.75 | 0.82 | 64 | empty |
| 3 | 72 | 0.74 | 0.98 | 19 | empty |
| 4 | 823 | 0.69 | 0.75 | 64 | empty |
| 5 | 406 | 0.61 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–C · 4023 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7BSP · Cryo-EM structure of a human ATP11C-CDC50A flippase in E1-AMPPCP state · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7BSP · PDBe 7BSP
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