Research workbench
Crystal structure of ATP11C-CDC50A in ptdser-bound E2P state
Analyse Crystal structure of ATP11C-CDC50A in ptdser-bound E2P state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKN
- Type
- protein
- Length
- 5,552 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipid-transporting ATPase ig; Cell cycle control protein 50A
- EC
- 7.6.2.1
- UniProt
- Q8NB49, Q9NV96
- Ligands
- P5S, AH2, NAG, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Phospholipid-transporting ATPase ig (EC 7.6.2.1) | protein | 1064 | 43% helix, 10% strand | Q8NB49 |
| C, F, J, N | Cell cycle control protein 50A | protein | 324 | 31% helix, 16% strand | Q9NV96 |
Ligands and binding sites
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · 7 copies · chains A, C, E, F, I, J, M, N
- AH2 · 1-deoxy-alpha-D-mannopyranose · ligand · 4 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains C, F, E, J, N
- MG · Magnesium ion · metal · 4 copies · chains A, E, I, M
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 | 339 | 0.86 | 0.95 | 54 | empty |
| 2 | 971 | 0.83 | 0.84 | 110 | empty |
| 3 | 527 | 0.83 | 0.88 | 55 | empty |
| 4 | 450 | 0.81 | 0.89 | 66 | empty |
| 5 | 1098 | 0.81 | 0.82 | 120 | empty |
Interfaces
12 interfaces between chains.
- A–C · 3953 Ų buried · 39 hydrogen bonds · protein-protein
- I–J · 3871 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 3852 Ų buried · 32 hydrogen bonds · protein-protein
- M–N · 3676 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 565 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 modified, 2 glycan, 1 covalent (disulfide, nonstandard, glycosylation, covalent ligand).
Compared structures
- 6LKN · Crystal structure of ATP11C-CDC50A in PtdSer-bound E2P state · the same entry in another collection · chain N against N, TM-score 1.00
- Q8NB49 · AlphaFold monomer V2.0 prediction for phospholipid-transporting ATPase ig (Q8NB49) · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q9NV96 · AlphaFold monomer V2.0 prediction for cell cycle control protein 50A (Q9NV96) · a predicted model of the same protein · chain F 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 Q8NB49
- Every structure of UniProt Q9NV96
- Elsewhere: RCSB PDB 6LKN · PDBe 6LKN · UniProt Q8NB49 · UniProt Q9NV96
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