Research workbench
Cryo-EM structure of patched in lipid nanodisc - the wildtype, 3.5 ångström (re-processed with dataset of 7DZQ)
Analyse Cryo-EM structure of patched in lipid nanodisc - the wildtype, 3.5 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V6Y
- Type
- protein
- Length
- 990 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein patched homolog 1,PROTEIN patched homolog 1
- UniProt
- Q61115
- Ligands
- CLR, 5VI, NAG
- Pockets
- 9 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein patched homolog 1,PROTEIN patched homolog 1 | protein | 990 | 57% helix, 6% strand | Q61115 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- 5VI · (2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.87 | 0.87 | 93 | CLR, 5VI |
| 2 | 84 | 0.74 | 0.96 | 21 | empty |
| 3 | 73 | 0.73 | 0.97 | 25 | empty |
| 4 | 340 | 0.59 | 0.77 | 41 | empty |
| 5 | 98 | 0.40 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7V6Y · Cryo-EM structure of Patched in lipid nanodisc - the wildtype, 3.5 angstrom (re-processed… · 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 7V6Y · PDBe 7V6Y · UniProt Q61115
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