Research workbench
Cryo-EM structure of DNF1 from saccharomyces cerevisiae in yeast lipids with amppcp ( resting state )
Analyse Cryo-EM structure of DNF1 from saccharomyces cerevisiae in yeast lipids with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DSI
- Type
- protein
- Length
- 1,507 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, P42838
- Ligands
- ACP, NAG, BMA, MG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 29% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase DNF1 (EC 7.6.2.1) | protein | 1145 | 33% helix, 10% strand | P32660 |
| B | Alkylphosphocholine resistance protein LEM3 | protein | 362 | 17% helix, 19% strand | P42838 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A
- BMA · beta-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
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.78 | 0.85 | 62 | ACP, MG |
| 2 | 845 | 0.76 | 0.80 | 71 | empty |
| 3 | 71 | 0.74 | 0.97 | 19 | empty |
| 4 | 544 | 0.70 | 0.79 | 58 | empty |
| 5 | 252 | 0.68 | 0.84 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 5019 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7DSI · Cryo-EM structure of Dnf1 from Saccharomyces cerevisiae in yeast lipids with AMPPCP (… · 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
- 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 0.69
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 P42838
- Elsewhere: RCSB PDB 7DSI · PDBe 7DSI · UniProt P32660 · UniProt P42838
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