Research workbench
Structure of the S. cerevisiae phosphatidylcholine flippase DNF2-LEM3 complex in the E1-ATP state
Analyse Structure of the S. cerevisiae phosphatidylcholine flippase DNF2-LEM3 complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KY8
- Type
- protein
- Length
- 1,274 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipid-transporting ATPase DNF2; Alkylphosphocholine resistance protein LEM3
- EC
- 7.6.2.1
- UniProt
- Q12675, P42838
- Ligands
- CLR, ACP, NAG, MAN, MG
- Pockets
- 19 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase DNF2 (EC 7.6.2.1) | protein | 910 | 51% helix, 11% strand | Q12675 |
| B | Alkylphosphocholine resistance protein LEM3 | protein | 364 | 24% helix, 19% strand | P42838 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 5 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.77 | 0.85 | 50 | MG, ACP |
| 2 | 465 | 0.67 | 0.78 | 48 | CLR |
| 3 | 242 | 0.57 | 0.78 | 39 | NAG |
| 4 | 159 | 0.54 | 0.80 | 27 | empty |
| 5 | 274 | 0.53 | 0.75 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 4803 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KY8 · Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the… · the same entry in another collection · chain A against A, TM-score 1.00
- P42838 · AlphaFold monomer V2.0 prediction for alkylphosphocholine resistance protein LEM3 (P42838) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q12675 · AlphaFold monomer V2.0 prediction for phospholipid-transporting ATPase DNF2 (Q12675) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 Q12675
- Every structure of UniProt P42838
- Elsewhere: RCSB PDB 7KY8 · PDBe 7KY8 · UniProt Q12675 · UniProt P42838
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