Research workbench
Hedgehog receptor patched (PTCH1) in complex with conformation selective nanobody TI23
Analyse Hedgehog receptor patched (PTCH1) in complex with conformation selective… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K65
- Type
- protein
- Length
- 1,120 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1; Nanobody TI23
- UniProt
- Q61115
- Ligands
- Q7G, NAG
- Pockets
- 13 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1 | protein | 1005 | 58% helix, 6% strand | Q61115 |
| B | Nanobody TI23 | protein | 115 | 5% helix, 43% strand | — |
Ligands and binding sites
- Q7G · 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta, 17beta,25r)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.84 | 0.85 | 88 | Q7G |
| 2 | 795 | 0.83 | 0.85 | 63 | Q7G |
| 3 | 240 | 0.72 | 0.87 | 34 | empty |
| 4 | 536 | 0.71 | 0.80 | 45 | empty |
| 5 | 285 | 0.62 | 0.80 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1261 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 7K65 · Hedgehog receptor Patched (PTCH1) in complex with conformation selective nanobody TI23 · the same entry in another collection · chain A against A, TM-score 1.00
- Q61115 · AlphaFold monomer V2.0 prediction for protein patched homolog 1 (Q61115) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q61115
- Elsewhere: RCSB PDB 7K65 · PDBe 7K65 · UniProt Q61115
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.