Research workbench
Structure of the S. cerevisiae phosphatidylcholine flippase DNF1-LEM3 complex in the apo E1 state
Analyse Structure of the S. cerevisiae phosphatidylcholine flippase DNF1-LEM3 complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KY6
- Type
- protein
- Length
- 1,322 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipid-transporting ATPase DNF1; Alkylphosphocholine resistance protein LEM3
- EC
- 7.6.2.1
- UniProt
- P32660, A0A6A5Q828
- Ligands
- NAG, MAN, MG
- Pockets
- 19 · best druggability 0.74
Structure
electron microscopy · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase DNF1 (EC 7.6.2.1) | protein | 957 | 56% helix, 12% strand | P32660 |
| B | Alkylphosphocholine resistance protein LEM3 | protein | 365 | 27% helix, 20% strand | A0A6A5Q828 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.74 | 0.79 | 76 | empty |
| 2 | 169 | 0.73 | 0.90 | 31 | empty |
| 3 | 67 | 0.69 | 0.95 | 18 | empty |
| 4 | 432 | 0.67 | 0.79 | 43 | empty |
| 5 | 212 | 0.56 | 0.79 | 31 | NAG |
Interfaces
1 interface between chains.
- A–B · 4932 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KY6 · Structure of the S. cerevisiae phosphatidylcholine flippase Dnf1-Lem3 complex in the apo… · the same entry in another collection · chain A against A, TM-score 1.00
- P32660 · AlphaFold monomer V2.0 prediction for phospholipid-transporting ATPase DNF1 (P32660) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P32660
- Every structure of UniProt A0A6A5Q828
- Elsewhere: RCSB PDB 7KY6 · PDBe 7KY6 · UniProt P32660 · UniProt A0A6A5Q828
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