Research workbench
Cryo-EM structure of human PTCH1 with three mutations L282Q/T500F/P504L
Analyse Cryo-EM structure of human PTCH1 with three mutations L282Q/T500F/P504L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DMO
- Type
- protein
- Length
- 982 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1
- UniProt
- Q13635
- Ligands
- NAG
- Pockets
- 17 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 53% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1 | protein | 982 | 53% helix, 6% strand | Q13635 |
Ligands and binding sites
- 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
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.86 | 0.87 | 112 | empty |
| 2 | 226 | 0.76 | 0.90 | 31 | empty |
| 3 | 59 | 0.69 | 0.96 | 16 | empty |
| 4 | 199 | 0.59 | 0.80 | 28 | empty |
| 5 | 79 | 0.57 | 0.87 | 25 | empty |
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6DMO · Cryo-EM structure of human Ptch1 with three mutations L282Q/T500F/P504L · the same entry in another collection · chain A against A, TM-score 1.00
- Q13635 · AlphaFold monomer V2.0 prediction for protein patched homolog 1 (Q13635) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q13635
- Elsewhere: RCSB PDB 6DMO · PDBe 6DMO · UniProt Q13635
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