MolNFT v1 · #162961 · protein
Cryo-EM structure of the autoinhibited DRS2P-CDC50P
6ROH · Probable phospholipid-transporting ATPase DRS2: “Cryo-EM structure of the autoinhibited DRS2P-CDC50P”. Electron microscopy, 4 ligands (PSF, NAG, BMA), 20 pockets (best druggability 0.75). MolNFT v1 #162961 on GenesisL1: 3D…
- PDB
- 6ROH
- Type
- protein
- Length
- 1,449 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
- PSF, NAG, BMA, MG
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable phospholipid-transporting ATPase DRS2 (EC 7.6.2.1) | protein | 1112 | 38% helix, 17% strand | P39524 |
| C | Cell division control protein 50 | protein | 337 | 20% helix, 20% strand | P25656 |
Ligands and binding sites
- PSF · 1,2-dicaproyl-sn-phosphatidyl-L-serine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains C
- 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.75 | 0.99 | 27 | empty |
| 2 | 512 | 0.74 | 0.82 | 47 | empty |
| 3 | 516 | 0.69 | 0.79 | 32 | PSF |
| 4 | 56 | 0.66 | 0.95 | 18 | empty |
| 5 | 281 | 0.64 | 0.81 | 34 | empty |
Interfaces
1 interface between chains.
- A–C · 4014 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 2 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 6ROH · Cryo-EM structure of the autoinhibited Drs2p-Cdc50p · the same entry in another collection · chain C against C, TM-score 1.00
- 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 0.99
- P25656 · AlphaFold monomer V2.0 prediction for cell division control protein 50 (P25656) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 6ROH · PDBe 6ROH · UniProt P39524 · UniProt P25656
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