Research workbench
Cryo-EM structure of murine dispatched 'T' conformation
Analyse Cryo-EM structure of murine dispatched 'T' conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RPI
- Type
- protein
- Length
- 926 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein dispatched homolog 1
- UniProt
- Q3TDN0
- Ligands
- Y01, AV0, NAG, NA
- Pockets
- 15 · best druggability 0.65
Structure
electron microscopy · 1 distinct chain · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein dispatched homolog 1 | protein | 926 | 59% helix, 8% strand | Q3TDN0 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 26 copies · chains A
- AV0 · 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.65 | 0.85 | 32 | empty |
| 2 | 195 | 0.63 | 0.83 | 23 | empty |
| 3 | 216 | 0.54 | 0.78 | 27 | Y01 |
| 4 | 113 | 0.54 | 0.83 | 21 | empty |
| 5 | 209 | 0.53 | 0.76 | 21 | Y01 |
Modifications
Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
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 Q3TDN0
- Elsewhere: RCSB PDB 7RPI · PDBe 7RPI · UniProt Q3TDN0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.