Research workbench
Cryo-EM structure of S. cerevisiae DRS2P-CDC50P in the PI4P-activated form
Analyse Cryo-EM structure of S. cerevisiae DRS2P-CDC50P in the PI4P-activated form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PSX
- Type
- protein
- Length
- 1,372 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable phospholipid-transporting ATPase DRS2; Cell division control protein 50
- EC
- 7.6.2.1
- UniProt
- P39524, P25656
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable phospholipid-transporting ATPase DRS2 (EC 7.6.2.1) | protein | 1033 | 41% helix, 14% strand | P39524 |
| E | Cell division control protein 50 | protein | 339 | 25% helix, 19% strand | P25656 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.78 | 0.80 | 81 | empty |
| 2 | 397 | 0.75 | 0.85 | 28 | empty |
| 3 | 1023 | 0.73 | 0.76 | 80 | empty |
| 4 | 50 | 0.69 | 0.97 | 21 | empty |
| 5 | 417 | 0.69 | 0.81 | 43 | empty |
Interfaces
1 interface between chains.
- A–E · 4165 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 6PSX · Cryo-EM structure of S. cerevisiae Drs2p-Cdc50p in the PI4P-activated form · the same entry in another collection · chain A against A, TM-score 1.00
- P25656 · AlphaFold monomer V2.0 prediction for cell division control protein 50 (P25656) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P39524 · AlphaFold monomer V2.0 prediction for probable phospholipid- transporting ATPase DRS2… · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P39524
- Every structure of UniProt P25656
- Elsewhere: RCSB PDB 6PSX · PDBe 6PSX · UniProt P39524 · UniProt P25656
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