Research workbench
CRYO_EM structure of delta N-NPC1L1-eze
Analyse CRYO_EM structure of delta N-NPC1L1-eze in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DFZ
- Type
- protein
- Length
- 897 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NPC1-like intracellular cholesterol transporter 1
- UniProt
- A0A0C4DFX6
- Ligands
- CLR, H56, NAG
- Pockets
- 8 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NPC1-like intracellular cholesterol transporter 1 | protein | 897 | 50% helix, 7% strand | A0A0C4DFX6 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 4 copies · chains A
- H56 · (3~{R},4~{S})-1-(4-fluorophenyl)-3-[(3~{S})-3-(4-fluorophenyl)-3-oxidanyl-propyl]-4-(4-hydroxyphenyl) azetidin-2-one · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.89 | 0.90 | 118 | H56 |
| 2 | 57 | 0.69 | 0.96 | 26 | empty |
| 3 | 60 | 0.53 | 0.87 | 18 | empty |
| 4 | 197 | 0.51 | 0.77 | 28 | empty |
| 5 | 144 | 0.51 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 10 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7DFZ · Cryo_EM structure of delta N-NPC1L1-EZE · 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 A0A0C4DFX6
- Elsewhere: RCSB PDB 7DFZ · PDBe 7DFZ · UniProt A0A0C4DFX6
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