MolNFT v1 · #180401 · protein
Structure of the S. cerevisiae phosphatidylcholine flippase DNF2-LEM3 complex in the E2P state
7KYA · Phospholipid-transporting ATPase DNF2: “Structure of the S. cerevisiae phosphatidylcholine flippase DNF2-LEM3 complex in the E2P state”. Electron microscopy, 5 ligands (CLR, BEF, NAG), 20 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 7KYA
- Type
- protein
- Length
- 1,545 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, BEF, NAG, MAN, MG
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase DNF2 (EC 7.6.2.1) | protein | 1174 | 43% helix, 15% strand | Q12675 |
| B | Alkylphosphocholine resistance protein LEM3 | protein | 371 | 23% helix, 16% strand | P42838 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 5 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · chains B
- MG · Magnesium ion · metal · 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 | 880 | 0.77 | 0.80 | 70 | empty |
| 2 | 770 | 0.75 | 0.80 | 77 | empty |
| 3 | 454 | 0.74 | 0.83 | 61 | empty |
| 4 | 76 | 0.74 | 0.97 | 22 | empty |
| 5 | 491 | 0.69 | 0.80 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 4876 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KYA · Structure of the S. cerevisiae phosphatidylcholine flippase Dnf2-Lem3 complex in the E2P… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.99
- 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 0.96
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 7KYA · PDBe 7KYA · UniProt Q12675 · UniProt P42838
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