Research workbench
Cryoem structure of mouse PCDH15-4EC-LHFPL5 complex
Analyse Cryoem structure of mouse PCDH15-4EC-LHFPL5 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C13
- Type
- protein
- Length
- 1,084 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin-15
- UniProt
- Q99PJ1
- Ligands
- NAG, MAN, BMA
- Pockets
- 10 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protocadherin-15 | protein | 542 | 10% helix, 34% strand | Q99PJ1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.80 | 0.81 | 83 | empty |
| 2 | 125 | 0.77 | 0.95 | 29 | empty |
| 3 | 132 | 0.77 | 0.94 | 26 | empty |
| 4 | 70 | 0.72 | 0.96 | 22 | empty |
| 5 | 111 | 0.61 | 0.87 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 2176 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan (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 Q99PJ1
- Elsewhere: RCSB PDB 6C13 · PDBe 6C13 · UniProt Q99PJ1
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