MolNFT v1 · #164904 · protein
Structure of drosophila melanogaster dispatched bound to a modified hedgehog ligand, hhn-C85II
6TD6 · Protein dispatched: “Structure of drosophila melanogaster dispatched bound to a modified hedgehog ligand, hhn-C85II”. Electron microscopy, 1 ligand (NAG), 19 pockets (best druggability 0.83). MolNFT v1 #164904 on GenesisL1: 3D…
- PDB
- 6TD6
- Type
- protein
- Length
- 982 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein dispatched; Protein hedgehog
- UniProt
- Q9VNJ5, Q02936
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein dispatched | protein | 842 | 61% helix, 5% strand | Q9VNJ5 |
| B | Protein hedgehog | protein | 140 | 28% helix, 19% strand | Q02936 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.83 | 0.89 | 58 | empty |
| 2 | 716 | 0.81 | 0.84 | 104 | empty |
| 3 | 972 | 0.78 | 0.80 | 118 | empty |
| 4 | 306 | 0.78 | 0.89 | 49 | empty |
| 5 | 284 | 0.78 | 0.89 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 650 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6TD6 · Structure of Drosophila melanogaster Dispatched bound to a modified Hedgehog ligand… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9VNJ5 · AlphaFold monomer V2.0 prediction for protein dispatched (Q9VNJ5) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q02936 · AlphaFold monomer V2.0 prediction for protein hedgehog (Q02936) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9VNJ5
- Every structure of UniProt Q02936
- Elsewhere: RCSB PDB 6TD6 · PDBe 6TD6 · UniProt Q9VNJ5 · UniProt Q02936
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.