MolNFT v1 · #156819 · protein
Crystal structure of human protocadherin-1 EC1-4 with glycosylation
6MGA: “Crystal structure of human protocadherin-1 EC1-4 with glycosylation”. X-ray diffraction, 3 ligands (NAG, MAN, CA), 2 pockets (best druggability 0.54). MolNFT v1 #156819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MGA
- Type
- protein
- Length
- 429 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocadherin-1
- UniProt
- Q08174
- Ligands
- NAG, MAN, CA
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocadherin-1 | protein | 429 | 6% helix, 45% strand | Q08174 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.54 | 0.87 | 15 | empty |
| 2 | 92 | 0.33 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 2 glycan, 1 disulfide (disulfide, N-glycosylation, O-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 Q08174
- Elsewhere: RCSB PDB 6MGA · PDBe 6MGA · UniProt Q08174
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