MolNFT v1 · #186781 · protein
Cryo-EM structure of murine dispatched 'R' conformation
7RPH · Protein dispatched homolog 1: “Cryo-EM structure of murine dispatched 'R' conformation”. Electron microscopy, 4 ligands (Y01, AV0, NAG), 12 pockets (best druggability 0.65). MolNFT v1 #186781 on GenesisL1: 3D structure, binding…
- PDB
- 7RPH
- 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
- 12 · best druggability 0.65
Structure
electron microscopy · 1 distinct chain · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein dispatched homolog 1 | protein | 926 | 61% 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 · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.65 | 0.80 | 52 | empty |
| 2 | 160 | 0.63 | 0.84 | 21 | empty |
| 3 | 277 | 0.54 | 0.76 | 30 | empty |
| 4 | 259 | 0.54 | 0.76 | 45 | empty |
| 5 | 198 | 0.50 | 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 7RPH · PDBe 7RPH · UniProt Q3TDN0
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