Research workbench
Cryo-EM structure of the activated DRS2P-CDC50P
Analyse Cryo-EM structure of the activated DRS2P-CDC50P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ROJ
- Type
- protein
- Length
- 1,404 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable phospholipid-transporting ATPase DRS2,OXALOACETATE decarboxylase alpha chain…
- EC
- 7.6.2.1, 7.2.4.2
- UniProt
- P39524, P13187, P25656
- Ligands
- 2Y5, NAG, BMA, MG
- Pockets
- 18 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable phospholipid-transporting ATPase DRS2,OXALOACETATE decarboxylase alpha chain (EC 7.6.2.1, 7.2.4.2) | protein | 1064 | 44% helix, 17% strand | P39524, P13187 |
| C | Cell division control protein 50 | protein | 340 | 24% helix, 21% strand | P25656 |
Ligands and binding sites
- 2Y5 · (2R)-1-{[(R)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy) propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C
- BMA · beta-D-mannopyranose · sugar · 4 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
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 | 739 | 0.79 | 0.83 | 73 | empty |
| 2 | 818 | 0.77 | 0.80 | 58 | empty |
| 3 | 59 | 0.71 | 0.98 | 20 | empty |
| 4 | 75 | 0.69 | 0.94 | 25 | empty |
| 5 | 164 | 0.65 | 0.86 | 32 | empty |
Interfaces
1 interface between chains.
- A–C · 4175 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 2 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 6ROJ · Cryo-EM structure of the activated Drs2p-Cdc50p · the same entry in another collection · chain A against A, 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 0.98
- 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 0.98
- P13187 · AlphaFold monomer V2.0 prediction for oxaloacetate decarboxylase alpha chain (P13187) · a predicted model of the same protein · chain A against A, TM-score 0.17
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 P13187
- Every structure of UniProt P25656
- Elsewhere: RCSB PDB 6ROJ · PDBe 6ROJ · UniProt P39524 · UniProt P13187 · UniProt P25656
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