MolNFT v1 · #155601 · protein
Cryo-EM structure of DNF1 from chaetomium thermophilum in the E1-ATP state
6LCR · Phospholipid-transporting ATPase: “Cryo-EM structure of DNF1 from chaetomium thermophilum in the E1-ATP state”. Electron microscopy, 5 ligands (ACP, P5S, NAG), 20 pockets (best druggability 0.68). MolNFT v1 #155601 on GenesisL1: 3D…
- PDB
- 6LCR
- Type
- protein
- Length
- 1,420 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
- ACP, P5S, NAG, BMA, MG
- Pockets
- 20 · best druggability 0.68
Structure
electron microscopy · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid-transporting ATPase (EC 7.6.2.1) | protein | 1044 | 47% helix, 14% strand | G0S196 |
| B | CDC50 | protein | 376 | 20% helix, 20% strand | G0SDN0 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · 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 · 9 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.68 | 0.78 | 51 | MG, ACP |
| 2 | 351 | 0.65 | 0.80 | 39 | empty |
| 3 | 503 | 0.64 | 0.76 | 54 | empty |
| 4 | 217 | 0.61 | 0.82 | 24 | P5S |
| 5 | 384 | 0.60 | 0.76 | 47 | NAG |
Interfaces
1 interface between chains.
- A–B · 4605 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 6LCR · Cryo-EM structure of Dnf1 from Chaetomium thermophilum in the E1-ATP 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 6LCR · PDBe 6LCR · UniProt G0S196 · UniProt G0SDN0
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