Research workbench
Cryo-EM structure of DNF1 from chaetomium thermophilum in the E2P state
Analyse Cryo-EM structure of DNF1 from chaetomium thermophilum in the E2P state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LCP
- Type
- protein
- Length
- 1,516 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipid-transporting ATPase; CDC50
- EC
- 7.6.2.1
- UniProt
- G0S196, G0SDN0
- Ligands
- POV, BEF, P5S, NAG, MAN, BMA, MG
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase (EC 7.6.2.1) | protein | 1140 | 45% helix, 14% strand | G0S196 |
| B | CDC50 | protein | 376 | 22% helix, 20% strand | G0SDN0 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 2 copies · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, A
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.78 | 0.81 | 82 | POV |
| 2 | 811 | 0.75 | 0.79 | 85 | empty |
| 3 | 70 | 0.72 | 0.97 | 20 | empty |
| 4 | 228 | 0.66 | 0.84 | 31 | P5S |
| 5 | 342 | 0.61 | 0.78 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 4600 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 6LCP · Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E2P state · the same entry in another collection · chain A against A, TM-score 1.00
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 G0S196
- Every structure of UniProt G0SDN0
- Elsewhere: RCSB PDB 6LCP · PDBe 6LCP · UniProt G0S196 · UniProt G0SDN0
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